Merge pull request #12 from lutzfischer/master

Version 1.6.715
Rappsilber-Laboratory · Apr 10, 2017 · 40e5057 · 40e5057
2 parents 5b2fc58 + 5b24392
commit 40e5057
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Showing 11 changed files with 780 additions and 78 deletions.
diff --git a/nbproject/build-impl.xml b/nbproject/build-impl.xml
@@ -79,43 +79,7 @@ is divided into following sections:
         <property file="nbproject/project.properties"/>
     </target>
     <target depends="-pre-init,-init-private,-init-libraries,-init-user,-init-project,-init-macrodef-property" name="-do-init">
-        <j2seproject1:property name="platform.home" value="platforms.${platform.active}.home"/>
-        <j2seproject1:property name="platform.bootcp" value="platforms.${platform.active}.bootclasspath"/>
-        <j2seproject1:property name="platform.compiler" value="platforms.${platform.active}.compile"/>
-        <j2seproject1:property name="platform.javac.tmp" value="platforms.${platform.active}.javac"/>
-        <condition property="platform.javac" value="${platform.home}/bin/javac">
-            <equals arg1="${platform.javac.tmp}" arg2="$${platforms.${platform.active}.javac}"/>
-        </condition>
-        <property name="platform.javac" value="${platform.javac.tmp}"/>
-        <j2seproject1:property name="platform.java.tmp" value="platforms.${platform.active}.java"/>
-        <condition property="platform.java" value="${platform.home}/bin/java">
-            <equals arg1="${platform.java.tmp}" arg2="$${platforms.${platform.active}.java}"/>
-        </condition>
-        <property name="platform.java" value="${platform.java.tmp}"/>
-        <j2seproject1:property name="platform.javadoc.tmp" value="platforms.${platform.active}.javadoc"/>
-        <condition property="platform.javadoc" value="${platform.home}/bin/javadoc">
-            <equals arg1="${platform.javadoc.tmp}" arg2="$${platforms.${platform.active}.javadoc}"/>
-        </condition>
-        <property name="platform.javadoc" value="${platform.javadoc.tmp}"/>
-        <condition property="platform.invalid" value="true">
-            <or>
-                <contains string="${platform.javac}" substring="$${platforms."/>
-                <contains string="${platform.java}" substring="$${platforms."/>
-                <contains string="${platform.javadoc}" substring="$${platforms."/>
-            </or>
-        </condition>
-        <fail unless="platform.home">Must set platform.home</fail>
-        <fail unless="platform.bootcp">Must set platform.bootcp</fail>
-        <fail unless="platform.java">Must set platform.java</fail>
-        <fail unless="platform.javac">Must set platform.javac</fail>
-        <fail if="platform.invalid">
- The J2SE Platform is not correctly set up.
- Your active platform is: ${platform.active}, but the corresponding property "platforms.${platform.active}.home" is not found in the project's properties files. 
- Either open the project in the IDE and setup the Platform with the same name or add it manually.
- For example like this:
-     ant -Duser.properties.file=&lt;path_to_property_file&gt; jar (where you put the property "platforms.${platform.active}.home" in a .properties file)
-  or ant -Dplatforms.${platform.active}.home=&lt;path_to_JDK_home&gt; jar (where no properties file is used) 
-  </fail>
+        <property name="platform.java" value="${java.home}/bin/java"/>
         <available file="${manifest.file}" property="manifest.available"/>
         <condition property="splashscreen.available">
             <and>
@@ -245,6 +209,20 @@ is divided into following sections:
         <condition else="" property="javac.profile.cmd.line.arg" value="-profile ${javac.profile}">
             <isset property="profile.available"/>
         </condition>
+        <condition else="false" property="jdkBug6558476">
+            <and>
+                <matches pattern="1\.[56]" string="${java.specification.version}"/>
+                <not>
+                    <os family="unix"/>
+                </not>
+            </and>
+        </condition>
+        <condition else="false" property="javac.fork">
+            <or>
+                <istrue value="${jdkBug6558476}"/>
+                <istrue value="${javac.external.vm}"/>
+            </or>
+        </condition>
         <property name="jar.index" value="false"/>
         <property name="jar.index.metainf" value="${jar.index}"/>
         <property name="copylibs.rebase" value="true"/>
@@ -314,7 +292,7 @@ is divided into following sections:
                 <property location="${build.dir}/empty" name="empty.dir"/>
                 <mkdir dir="${empty.dir}"/>
                 <mkdir dir="@{apgeneratedsrcdir}"/>
-                <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" executable="${platform.javac}" fork="yes" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
+                <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
                     <src>
                         <dirset dir="@{gensrcdir}" erroronmissingdir="false">
                             <include name="*"/>
@@ -354,7 +332,7 @@ is divided into following sections:
             <sequential>
                 <property location="${build.dir}/empty" name="empty.dir"/>
                 <mkdir dir="${empty.dir}"/>
-                <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" executable="${platform.javac}" fork="yes" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
+                <javac debug="@{debug}" deprecation="${javac.deprecation}" destdir="@{destdir}" encoding="${source.encoding}" excludes="@{excludes}" fork="${javac.fork}" includeantruntime="false" includes="@{includes}" source="${javac.source}" sourcepath="@{sourcepath}" srcdir="@{srcdir}" target="${javac.target}" tempdir="${java.io.tmpdir}">
                     <src>
                         <dirset dir="@{gensrcdir}" erroronmissingdir="false">
                             <include name="*"/>
@@ -435,7 +413,7 @@ is divided into following sections:
             <element name="customize" optional="true"/>
             <sequential>
                 <property name="junit.forkmode" value="perTest"/>
-                <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
+                <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
                     <test methods="@{testmethods}" name="@{testincludes}" todir="${build.test.results.dir}"/>
                     <syspropertyset>
                         <propertyref prefix="test-sys-prop."/>
@@ -458,7 +436,7 @@ is divided into following sections:
             <element name="customize" optional="true"/>
             <sequential>
                 <property name="junit.forkmode" value="perTest"/>
-                <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
+                <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
                     <batchtest todir="${build.test.results.dir}">
                         <fileset dir="${test.src.dir}" excludes="@{excludes},${excludes}" includes="@{includes}">
                             <filename name="@{testincludes}"/>
@@ -497,7 +475,7 @@ is divided into following sections:
                     </fileset>
                 </union>
                 <taskdef classname="org.testng.TestNGAntTask" classpath="${run.test.classpath}" name="testng"/>
-                <testng classfilesetref="test.set" failureProperty="tests.failed" jvm="${platform.java}" listeners="org.testng.reporters.VerboseReporter" methods="${testng.methods.arg}" mode="${testng.mode}" outputdir="${build.test.results.dir}" suitename="XiSearch" testname="TestNG tests" workingDir="${work.dir}">
+                <testng classfilesetref="test.set" failureProperty="tests.failed" listeners="org.testng.reporters.VerboseReporter" methods="${testng.methods.arg}" mode="${testng.mode}" outputdir="${build.test.results.dir}" suitename="XiSearch" testname="TestNG tests" workingDir="${work.dir}">
                     <xmlfileset dir="${build.test.classes.dir}" includes="@{testincludes}"/>
                     <propertyset>
                         <propertyref prefix="test-sys-prop."/>
@@ -577,7 +555,7 @@ is divided into following sections:
             <element name="customize" optional="true"/>
             <sequential>
                 <property name="junit.forkmode" value="perTest"/>
-                <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
+                <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
                     <test methods="@{testmethods}" name="@{testincludes}" todir="${build.test.results.dir}"/>
                     <syspropertyset>
                         <propertyref prefix="test-sys-prop."/>
@@ -602,7 +580,7 @@ is divided into following sections:
             <element name="customize" optional="true"/>
             <sequential>
                 <property name="junit.forkmode" value="perTest"/>
-                <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" jvm="${platform.java}" showoutput="true" tempdir="${build.dir}">
+                <junit dir="${work.dir}" errorproperty="tests.failed" failureproperty="tests.failed" fork="true" forkmode="${junit.forkmode}" showoutput="true" tempdir="${build.dir}">
                     <batchtest todir="${build.test.results.dir}">
                         <fileset dir="${test.src.dir}" excludes="@{excludes},${excludes}" includes="@{includes}">
                             <filename name="@{testincludes}"/>
@@ -782,9 +760,6 @@ is divided into following sections:
                     <classpath>
                         <path path="@{classpath}"/>
                     </classpath>
-                    <bootclasspath>
-                        <path path="${platform.bootcp}"/>
-                    </bootclasspath>
                 </nbjpdastart>
             </sequential>
         </macrodef>
@@ -800,9 +775,7 @@ is divided into following sections:
         </macrodef>
     </target>
     <target name="-init-debug-args">
-        <exec executable="${platform.java}" outputproperty="version-output">
-            <arg value="-version"/>
-        </exec>
+        <property name="version-output" value="java version &quot;${ant.java.version}"/>
         <condition property="have-jdk-older-than-1.4">
             <or>
                 <contains string="${version-output}" substring="java version &quot;1.0"/>
@@ -827,7 +800,7 @@ is divided into following sections:
             <attribute default="${debug.classpath}" name="classpath"/>
             <element name="customize" optional="true"/>
             <sequential>
-                <java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true" jvm="${platform.java}">
+                <java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true">
                     <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
                     <jvmarg line="${debug-args-line}"/>
                     <jvmarg value="-Xrunjdwp:transport=${debug-transport},address=${jpda.address}"/>
@@ -854,7 +827,7 @@ is divided into following sections:
             <attribute default="jvm" name="jvm"/>
             <element name="customize" optional="true"/>
             <sequential>
-                <java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true" jvm="${platform.java}">
+                <java classname="@{classname}" dir="${work.dir}" failonerror="${java.failonerror}" fork="true">
                     <jvmarg line="${endorsed.classpath.cmd.line.arg}"/>
                     <jvmarg value="-Dfile.encoding=${runtime.encoding}"/>
                     <redirector errorencoding="${runtime.encoding}" inputencoding="${runtime.encoding}" outputencoding="${runtime.encoding}"/>
@@ -1052,7 +1025,7 @@ is divided into following sections:
         <j2seproject3:copylibs manifest="${tmp.manifest.file}"/>
         <echo level="info">To run this application from the command line without Ant, try:</echo>
         <property location="${dist.jar}" name="dist.jar.resolved"/>
-        <echo level="info">${platform.java} -jar "${dist.jar.resolved}"</echo>
+        <echo level="info">java -jar "${dist.jar.resolved}"</echo>
     </target>
     <target depends="init,compile,-pre-pre-jar,-pre-jar,-do-jar-create-manifest,-do-jar-copy-manifest,-do-jar-set-mainclass,-do-jar-set-profile,-do-jar-set-splashscreen" if="do.archive" name="-do-jar-jar" unless="do.mkdist">
         <j2seproject1:jar manifest="${tmp.manifest.file}"/>
@@ -1261,13 +1234,10 @@ is divided into following sections:
                 </not>
             </and>
         </condition>
-        <exec executable="${platform.java}" failonerror="false" outputproperty="platform.version.output">
-            <arg value="-version"/>
-        </exec>
         <condition else="" property="bug5101868workaround" value="*.java">
-            <matches multiline="true" pattern="1\.[56](\..*)?" string="${platform.version.output}"/>
+            <matches pattern="1\.[56](\..*)?" string="${java.version}"/>
         </condition>
-        <javadoc additionalparam="-J-Dfile.encoding=${file.encoding} ${javadoc.additionalparam}" author="${javadoc.author}" charset="UTF-8" destdir="${dist.javadoc.dir}" docencoding="UTF-8" encoding="${javadoc.encoding.used}" executable="${platform.javadoc}" failonerror="true" noindex="${javadoc.noindex}" nonavbar="${javadoc.nonavbar}" notree="${javadoc.notree}" private="${javadoc.private}" source="${javac.source}" splitindex="${javadoc.splitindex}" use="${javadoc.use}" useexternalfile="true" version="${javadoc.version}" windowtitle="${javadoc.windowtitle}">
+        <javadoc additionalparam="-J-Dfile.encoding=${file.encoding} ${javadoc.additionalparam}" author="${javadoc.author}" charset="UTF-8" destdir="${dist.javadoc.dir}" docencoding="UTF-8" encoding="${javadoc.encoding.used}" failonerror="true" noindex="${javadoc.noindex}" nonavbar="${javadoc.nonavbar}" notree="${javadoc.notree}" private="${javadoc.private}" source="${javac.source}" splitindex="${javadoc.splitindex}" use="${javadoc.use}" useexternalfile="true" version="${javadoc.version}" windowtitle="${javadoc.windowtitle}">
             <classpath>
                 <path path="${javac.classpath}"/>
             </classpath>

diff --git a/nbproject/genfiles.properties b/nbproject/genfiles.properties
@@ -1,8 +1,8 @@
-build.xml.data.CRC32=fd898e9c
+build.xml.data.CRC32=be8a7bc0
 build.xml.script.CRC32=3dec13ec
 build.xml.stylesheet.CRC32=[email protected]
 # This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
 # Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
-nbproject/build-impl.xml.data.CRC32=fd898e9c
-nbproject/build-impl.xml.script.CRC32=6eb89762
+nbproject/build-impl.xml.data.CRC32=be8a7bc0
+nbproject/build-impl.xml.script.CRC32=f54f9770
 nbproject/build-impl.xml.stylesheet.CRC32=[email protected]
diff --git a/nbproject/private/profiler/attach.xml b/nbproject/private/profiler/attach.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd">
+<properties>
+<comment/>
+<entry key="profiler.attach.dynamic.pid">4841</entry>
+<entry key="profiler.attach.remote">false</entry>
+<entry key="profiler.attach.server.type">Java application</entry>
+<entry key="profiler.attach.dynamic.jdk16">true</entry>
+<entry key="profiler.attach.direct">false</entry>
+<entry key="profiler.attach.target.type">Java application</entry>
+<entry key="profiler.attach.dynamic.processName">rappsilber.gui.XiDBStarter</entry>
+<entry key="profiler.attach.host"/>
+</properties>
diff --git a/nbproject/private/profiler/settings.xml b/nbproject/private/profiler/settings.xml
@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE properties SYSTEM "http://java.sun.com/dtd/properties.dtd">
+<properties>
+<comment/>
+<entry key="ACTIVATED_FEATURES">#org.netbeans.modules.profiler.v2.features.ThreadsFeature@#org.netbeans.modules.profiler.v2.features.MonitorFeature@#org.netbeans.modules.profiler.v2.features.MethodsFeature@</entry>
+<entry key="SINGLE_FEATURE">false</entry>
+</properties>
diff --git a/nbproject/project.properties b/nbproject/project.properties
@@ -79,7 +79,7 @@ manifest.custom.permissions=
 manifest.file=manifest.mf
 meta.inf.dir=${src.dir}/META-INF
 mkdist.disabled=false
-platform.active=JDK_1.7
+platform.active=default_platform
 project.license=apache20
 run.classpath=\
     ${javac.classpath}:\

diff --git a/nbproject/project.xml b/nbproject/project.xml
@@ -4,7 +4,6 @@
     <configuration>
         <data xmlns="http://www.netbeans.org/ns/j2se-project/3">
             <name>XiSearch</name>
-            <explicit-platform explicit-source-supported="true"/>
             <source-roots>
                 <root id="src.dir"/>
             </source-roots>

diff --git a/src/rappsilber/applications/SimpleXiProcessLinearIncluded.java b/src/rappsilber/applications/SimpleXiProcessLinearIncluded.java
@@ -180,7 +180,13 @@ protected void fragmentTree() {
         setStatus("Build Fragmenttree - splitting by peptide mass");
         Logger.getLogger(SimpleXiProcess.class.getName()).log(Level.INFO, "Build Fragment Tree - splitting by peptide mass");
 //        m_Fragments = new rappsilber.ms.lookup.fragments.FragmentTreeSlimedMTvArrayOnly(m_peptides, getSequenceList(), getCPUs(), getConfig());
-        m_Fragments = new rappsilber.ms.lookup.fragments.FragmentTreeSlimedArrayMassSplitBuild(m_peptides, getSequenceList(), getCPUs(), getConfig());
+
+        String tree = getConfig().retrieveObject("FRAGMENTTREE", "default").toLowerCase();
+        if (tree.contentEquals("default")) {
+            m_Fragments = new rappsilber.ms.lookup.fragments.FragmentTreeSlimedArrayMassSplitBuild(m_peptides, getSequenceList(), getCPUs(), getConfig());
+        } else if (tree.contentEquals("int")) {
+            m_Fragments = new rappsilber.ms.lookup.fragments.FragmentTreeSlimedIntArray(m_peptides, getSequenceList(), getCPUs(), getConfig());
+        }
 //        m_Fragments = new rappsilber.ms.lookup.fragments.FragmentMapDB(m_peptides, getSequenceList(), getCPUs(), getConfig());
     }
 

diff --git a/src/rappsilber/applications/SimpleXiProcessOpenModificationXlink.java b/src/rappsilber/applications/SimpleXiProcessOpenModificationXlink.java
@@ -18,6 +18,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -291,7 +292,14 @@ public void process(SpectraAccess input, ResultWriter output) {
                 // for some spectra we are not sure of the charge state
                 // so we have to considere every possible one for these
                 // spectraAllchargeStatess
-                for (Spectra spectra : spectraAllchargeStatess.getChargeStateSpectra()) {
+
+                Collection<Spectra> specs;
+                if (isRelaxedPrecursorMatching())
+                    specs = spectraAllchargeStatess.getRelaxedAlternativeSpectra();
+                else
+                    specs = spectraAllchargeStatess.getAlternativeSpectra();
+
+                for (Spectra spectra : specs) {
                     HashMapList<Peptide,Peptide> alphaPeptides = new HashMapList<Peptide, Peptide>();