From 0c8315632019a6e3704d868cdc9d6d212f0df79a Mon Sep 17 00:00:00 2001
From: DDred <avs110@inbox.ru>
Date: Fri, 22 Jul 2011 14:09:59 +0000
Subject: [PATCH]

---
 .idea/misc.xml                                |  3 +++
 .../com/rapidminer/resources/OperatorsHMM.xml | 26 ++++++++++++++++---
 src/libiada/IntervalAnalysis/Chain.java       | 20 ++++++++++++++
 .../IntervalAnalysis/UniformChain.java        |  2 +-
 4 files changed, 46 insertions(+), 5 deletions(-)

diff --git a/.idea/misc.xml b/.idea/misc.xml
index 6c400ec..113aadf 100644
--- a/.idea/misc.xml
+++ b/.idea/misc.xml
@@ -23,6 +23,9 @@
     <option name="LOCALE" />
     <option name="OPEN_IN_BROWSER" value="true" />
   </component>
+  <component name="ProjectResources">
+    <default-html-doctype>http://www.w3.org/1999/xhtml</default-html-doctype>
+  </component>
   <component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true" project-jdk-name="1.6" project-jdk-type="JavaSDK">
     <output url="file://$PROJECT_DIR$/out" />
   </component>
diff --git a/resources/com/rapidminer/resources/OperatorsHMM.xml b/resources/com/rapidminer/resources/OperatorsHMM.xml
index 68f9279..1c20b80 100644
--- a/resources/com/rapidminer/resources/OperatorsHMM.xml
+++ b/resources/com/rapidminer/resources/OperatorsHMM.xml
@@ -6,7 +6,13 @@
                 <group key="reader">
                     <operator>
                         <key>FASTAReader</key>
-                        <class>Bio.RapidMiner.FASTAReaderRM</class>
+                        <class>rapidminer.Bioinformatics.FASTAReaderRM</class>
+                    </operator>
+                </group>
+                <group key="ORF">
+                    <operator>
+                        <key>ORFFinder</key>
+                        <class>rapidminer.Bioinformatics.ORMFinderRM</class>
                     </operator>
                 </group>
             </group>
@@ -17,6 +23,10 @@
                     <key>Building characteristic</key>
                     <class>rapidminer.BuildingCharacteristicRM</class>
                 </operator>
+                <operator>
+                    <key>UBuilding characteristic</key>
+                    <class>rapidminer.chain.UBuildingCharacteristicRM</class>
+                </operator>
             </group>
             <group key="readers">
                 <operator>
@@ -36,13 +46,21 @@
                     </operator>
                 </group>
                 <operator>
-                    <key>Buildings counter</key>
-                    <class>interval_analysis.chain.RMBuildingCounter</class>
+                    <key>Event recombination</key>
+                    <class>rapidminer.chain.EventRecombinationRM</class>
                 </operator>
                 <operator>
-                    <key>Mixed_converter</key>
+                    <key>Mixed converter</key>
                     <class>rapidminer.chain.MixedConverterRM</class>
                 </operator>
+                <operator>
+                    <key>Chain decompositor</key>
+                    <class>rapidminer.chain.Decompositor.ChainDecompositorRM</class>
+                </operator>
+                <operator>
+                    <key>Buildings counter</key>
+                    <class>rapidminer.chain.RMBuildingCounter</class>
+                </operator>
             </group>
             <group key="contents">
                 <group key="generators">
diff --git a/src/libiada/IntervalAnalysis/Chain.java b/src/libiada/IntervalAnalysis/Chain.java
index e6063ea..cd5215c 100644
--- a/src/libiada/IntervalAnalysis/Chain.java
+++ b/src/libiada/IntervalAnalysis/Chain.java
@@ -91,4 +91,24 @@ public double injectIntoCharacteristic(Class<? extends ICharacteristicCalculator
     public ChainWithCharacteristic getUniformChain(IBaseObject baseObject) {
         return null;  //TODO:"Fill method"
     }
+
+    public ChainWithCharacteristicSet getDecomposition(int wordLength, int step) throws Exception {
+        ChainWithCharacteristicSet chSet = new ChainWithCharacteristicSet();
+        int currentPos = 0;
+        int wordCount = Math.round((getLength() - wordLength) / step);
+        /*if (step == 1) {
+            wordCount -= (wordLength - 1);
+        }*/
+        for (int j = 0; j <= wordCount; j++) {
+            Chain ch = new Chain(wordLength);
+            int newWordPos = 0;
+            for (int i = currentPos; i < currentPos + wordLength; i++) {
+                ch.add(this.get(i), newWordPos);
+                newWordPos++;
+            }
+            currentPos += step;
+            chSet.add(ch);
+        }
+        return chSet;
+    }
 }
diff --git a/src/libiada/IntervalAnalysis/UniformChain.java b/src/libiada/IntervalAnalysis/UniformChain.java
index 30785ab..2527d1e 100644
--- a/src/libiada/IntervalAnalysis/UniformChain.java
+++ b/src/libiada/IntervalAnalysis/UniformChain.java
@@ -57,7 +57,7 @@ protected void buildIntervals() throws Exception {
     private int getRight(int current) {
         for (int i = current + 1; i < getLength(); i++)
         {
-            if (vault.get(i) == 1)
+            if (vault.get(i) == getAlpahbet().getPower()-1)
             {
                 return i;
             }