moved visible sub-alignment extraction and update from MsaWSThread to

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 054896b..272d81d 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -41,9 +41,7 @@ public class SequenceGroup
     boolean displayBoxes;\r
     boolean displayText;\r
     boolean colourText;\r
-\r
-    /** DOCUMENT ME!! */\r
-    public Vector sequences = new Vector();\r
+    private Vector sequences = new Vector();\r
     int width = -1;\r
 \r
     /** DOCUMENT ME!! */\r
@@ -115,6 +113,89 @@ public class SequenceGroup
         endRes = end;\r
     }\r
 \r
+    public SequenceI [] getSelectionAsNewSequences(AlignmentI align)\r
+    {\r
+      int iSize = sequences.size();\r
+      SequenceI [] seqs = new SequenceI[iSize];\r
+      SequenceI [] inorder = getSequencesInOrder(align);\r
+\r
+    char ch;\r
+    int sres, eres;\r
+\r
+    for (int i = 0; i < iSize; i++)\r
+    {\r
+      SequenceI seq = inorder[i];\r
+\r
+      //FIND START RES\r
+      //Returns residue following index if gap\r
+      sres = seq.findPosition(startRes);\r
+\r
+      //FIND END RES\r
+      //Need to find the residue preceeding index if gap\r
+      eres = 0;\r
+\r
+      for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)\r
+      {\r
+        ch = seq.getCharAt(j);\r
+        if (!jalview.util.Comparison.isGap( (ch)))\r
+        {\r
+          eres++;\r
+        }\r
+      }\r
+\r
+      if (eres > 0)\r
+      {\r
+        eres += seq.getStart() - 1;\r
+      }\r
+\r
+      seqs[i] = new Sequence(seq.getName(),\r
+                             seq.getSequence(startRes, endRes + 1),\r
+                             sres,\r
+                             eres);\r
+      seqs[i].setDescription(seq.getDescription());\r
+      seqs[i].setDBRef(seq.getDBRef());\r
+      seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
+      if (seq.getDatasetSequence() != null)\r
+        seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+\r
+      if(seq.getAnnotation()!=null)\r
+      {\r
+        for(int a=0; a<seq.getAnnotation().length; a++)\r
+          seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);\r
+      }\r
+    }\r
+\r
+    return seqs;\r
+\r
+    }\r
+\r
+    public Vector getSequences(boolean includeHidden)\r
+    {\r
+      if(!includeHidden)\r
+        return sequences;\r
+      else\r
+      {\r
+        Vector allSequences = new Vector();\r
+        SequenceI seq;\r
+        for (int i = 0; i < sequences.size(); i++)\r
+        {\r
+          seq = (SequenceI) sequences.elementAt(i);\r
+          allSequences.addElement(seq);\r
+          if (seq.getHiddenSequences() != null)\r
+          {\r
+            for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)\r
+            {\r
+              allSequences.addElement(\r
+                  seq.getHiddenSequences().getSequenceAt(h)\r
+                  );\r
+            }\r
+          }\r
+        }\r
+\r
+        return allSequences;\r
+      }\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -235,32 +316,40 @@ public class SequenceGroup
      */\r
     public void recalcConservation()\r
     {\r
-        if (cs != null)\r
-        {\r
-            cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
-        }\r
+        if(cs == null)\r
+          return;\r
 \r
-        if (cs instanceof ClustalxColourScheme)\r
+        try\r
         {\r
-            ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
-        }\r
+          cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));\r
 \r
-        if (cs instanceof ConservationColourScheme)\r
-        {\r
+          if (cs instanceof ClustalxColourScheme)\r
+          {\r
+            ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());\r
+          }\r
+\r
+          if (cs.conservationApplied())\r
+          {\r
             Conservation c = new Conservation(groupName,\r
-                    ResidueProperties.propHash, 3, sequences, 0, getWidth());\r
+                                              ResidueProperties.propHash, 3, sequences,\r
+                                              0, getWidth());\r
             c.calculate();\r
             c.verdict(false, 25);\r
 \r
-            ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
-            ccs.conserve = c;\r
+            cs.setConservation(c);\r
 \r
-            if (ccs.cs instanceof ClustalxColourScheme)\r
+            if (cs instanceof ClustalxColourScheme)\r
             {\r
-                ((ClustalxColourScheme) ccs.cs).resetClustalX(sequences,\r
-                    getWidth());\r
+              ( (ClustalxColourScheme) cs).resetClustalX(sequences,\r
+                                                         getWidth());\r
             }\r
+          }\r
+        }\r
+        catch (java.lang.OutOfMemoryError err)\r
+        {\r
+          System.out.println("Out of memory loading groups: " + err);\r
         }\r
+\r
     }\r
 \r
     /**\r
@@ -342,9 +431,24 @@ public class SequenceGroup
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public int getSize()\r
+    public int getSize(boolean includeHidden)\r
     {\r
+      if(!includeHidden)\r
         return sequences.size();\r
+      else\r
+      {\r
+        int total = sequences.size();\r
+        SequenceI seq;\r
+        for (int i = 0; i < sequences.size(); i++)\r
+        {\r
+          seq = (SequenceI) sequences.elementAt(i);\r
+          if (seq.getHiddenSequences() != null)\r
+          {\r
+            total += seq.getHiddenSequences().getSize(false);\r
+          }\r
+        }\r
+        return total;\r
+      }\r
     }\r
 \r
     /**\r