v1.0.5

- Now we can manage projects without coding transcripts.
- Updated GO.obo file.
- Improved insertion of TranscriptInformation if it is not present in the GFF3.
- DFI bugs fixed.

DbAnnotation.java

@@ -84,6 +84,7 @@ public class DbAnnotation  extends DbBase {
     private final String sqlSelTrans = "SELECT DISTINCT(SeqName) FROM " + tblAnnotations;
     //private final String sqlSelTransStrand = "SELECT DISTINCT(SeqName), Strand FROM " + tblAnnotations + " WHERE Strand LIKE '+' OR Strand LIKE '-';";
     private final String sqlSelTransStrand = "SELECT DISTINCT(T1.SeqName), T1.Strand, T2.Start, T2.End FROM " +  tblAnnotations + " as T1 LEFT JOIN (SELECT * FROM " + tblAnnotations + " as T3 WHERE T3.Feature LIKE 'CDS') as T2 ON (T1.SeqName = T2.SeqName) WHERE T1.Strand LIKE '+' OR T1.Strand LIKE '-';";
+    private final String sqlSelTransWithCDS = "SELECT DISTINCT(SeqName), Strand, Start, End FROM " +  tblAnnotations + " WHERE Feature LIKE 'CDS' AND Start-End !=0;";
     private final String sqlSelTransLength = "SELECT SeqName, Length FROM " + tblAnnotations + " WHERE Feature = 'transcript'";
     private final String sqlSelLengthAnnotations = "SELECT max(rowId) FROM " + tblAnnotations + ";";
     private final String sqlSelExistStructural = "SELECT SeqName FROM " + tblAnnotations + " WHERE Source LIKE '" + STRUCTURAL_SOURCE + "' LIMIT 1";
@@ -386,7 +387,7 @@ public String insertNewFeatures(String feature){
     // 1=3UTR length, 2 = 5UTR length, 3=CDS length, 4=polyASite
     public boolean insertNewAnnot(int i){
         boolean result = false;
-        ResultSet rs = getRS(sqlSelTransStrand);
+        ResultSet rs = getRS(sqlSelTransWithCDS);
         String lstTrans = "";
         String feature = "";
         String length = null, start = null, end = null, desc = "", total = "";
@@ -418,6 +419,10 @@ public boolean insertNewAnnot(int i){
 //                                eq = eq + 0.1;
 //                            }
                             count++;
+                            //check if is coding
+                            String seq = rs.getString("SeqName");
+
+
                             switch(i){
                                 case(1): length = genomicPos.get(rs.getString("SeqName"));
                                     total = totalLength.get(rs.getString("SeqName"));

DbProject.java

@@ -821,9 +821,17 @@ private boolean populateIdsTable() {
                         result = true;
                     else
                         logger.logError("No DB gene ids records added." );
+                }else{
+                    logger.logInfo("No DB protein records added." ); //before was an error but can be data without proteins
+                    sql = sqlInsGenes.replace("<S>", project.data.getAnnotationFileDefs().gene.source);
+                    sql = sql.replace("<F>", project.data.getAnnotationFileDefs().gene.feature);
+                    rowcnt = stmt.executeUpdate(sql);
+                    System.out.println("Inserted " + rowcnt + " rows into " + tblGenes);
+                    if(rowcnt > 0)
+                        result = true;
+                    else
+                        logger.logError("No DB gene ids records added.");
                 }
-                else
-                    logger.logError("No DB protein records added." );
             } catch ( Exception e ) {
                 logger.logError(e.getClass().getName() + " Code Exception: " + e.getMessage() );
 

Tappas.java

@@ -51,7 +51,7 @@ public class Tappas extends Application {
     public static final String APP_NAME = "tappas";
     public static final int APP_MAJOR_VER = 1;
     public static final int APP_MINOR_VER = 0;
-    public static final int APP_STRREV = 4;
+    public static final int APP_STRREV = 5;
     public static final String RES_VER_FILE = "resource_v" + APP_MAJOR_VER + "." + APP_MINOR_VER + "." + APP_STRREV + ".txt";
     public static final String APP_LOCK_FILE = ".tappas.lock.prm";
     public static final String APP_PORT_PARAM = "port";