IgnoreGapsConsensus

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index aeee116..db1f9c9 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -80,6 +80,7 @@ public class AlignFrame
       }\r
     }\r
 \r
+\r
   }\r
 \r
   public void inputText_actionPerformed(ActionEvent e)\r
@@ -278,30 +279,55 @@ public class AlignFrame
       orderedSeqs.put(index + "", seq);\r
     }\r
 \r
-    int index = 0;\r
+    int index = 0, startRes, endRes;\r
+    char ch;\r
+\r
     for (int i = 0; i < sg.getSize(); i++)\r
     {\r
-      SequenceI seq = null;\r
-      while (seq == null)\r
-      {\r
-        if (orderedSeqs.containsKey(index + ""))\r
+        SequenceI seq = null;\r
+\r
+        while (seq == null)\r
         {\r
-          seq = (SequenceI) orderedSeqs.get(index + "");\r
-          index++;\r
-          break;\r
+            if (orderedSeqs.containsKey(index + ""))\r
+            {\r
+                seq = (SequenceI) orderedSeqs.get(index + "");\r
+                index++;\r
+\r
+                break;\r
+            }\r
+            else\r
+            {\r
+                index++;\r
+            }\r
         }\r
-        else\r
+\r
+        //FIND START RES\r
+        //Returns residue following index if gap\r
+        startRes = seq.findPosition(sg.getStartRes());\r
+\r
+        //FIND END RES\r
+        //Need to find the residue preceeding index if gap\r
+        endRes = 0;\r
+\r
+        for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
         {\r
-          index++;\r
+          ch = seq.getCharAt(j);\r
+          if (!jalview.util.Comparison.isGap( (ch)))\r
+          {\r
+            endRes++;\r
+          }\r
+        }\r
+\r
+        if(endRes>0)\r
+        {\r
+          endRes += seq.getStart() -1;\r
         }\r
-      }\r
 \r
-      copiedSequences.append(seq.getName() + "\t" +\r
-                             seq.findPosition(sg.getStartRes()) + "\t"\r
-                             + seq.findPosition(sg.getEndRes()) + "\t"\r
-                             +\r
-                             sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
-          sg.getEndRes() + 1) + "\n");\r
+        copiedSequences.append(seq.getName() + "\t" +\r
+            startRes + "\t" +\r
+            endRes + "\t" +\r
+            seq.getSequence(sg.getStartRes(),\r
+                sg.getEndRes() + 1) + "\n");\r
     }\r
 \r
   }\r
@@ -397,13 +423,26 @@ public class AlignFrame
       return;\r
     }\r
 \r
+\r
     SequenceGroup sg = viewport.getSelectionGroup();\r
+    boolean allSequences = false;\r
+    if(sg.sequences.size()==viewport.alignment.getHeight())\r
+          allSequences = true;\r
+\r
     for (int i = 0; i < sg.sequences.size(); i++)\r
     {\r
       SequenceI seq = sg.getSequenceAt(i);\r
       int index = viewport.getAlignment().findIndex(seq);\r
       seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
 \r
+      // If the cut affects all sequences, remove highlighted columns\r
+      if (allSequences)\r
+      {\r
+        viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+                                                     sg.getEndRes() + 1);\r
+      }\r
+\r
+\r
       if (seq.getSequence().length() < 1)\r
       {\r
         viewport.getAlignment().deleteSequence(seq);\r
@@ -554,7 +593,9 @@ public class AlignFrame
 \r
     int start=0, end = viewport.alignment.getWidth();\r
 \r
-    if(viewport.getSelectionGroup()!=null)\r
+    if (viewport.getSelectionGroup() != null\r
+        && viewport.getSelectionGroup().sequences != null\r
+        && viewport.getSelectionGroup().sequences.size()>0)\r
     {\r
       seqs = viewport.getSelectionGroup().sequences;\r
       start = viewport.getSelectionGroup().getStartRes();\r
@@ -579,7 +620,7 @@ public class AlignFrame
         }\r
         j++;\r
       }\r
-      while(j < end);\r
+      while(j < end && j < jSize) ;\r
     }\r
 \r
     viewport.updateConservation();\r
@@ -767,14 +808,14 @@ public class AlignFrame
 \r
       if (cs instanceof ResidueColourScheme)\r
       {\r
-        ( (ResidueColourScheme) cs).setThreshold(threshold);\r
+        ( (ResidueColourScheme) cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
       }\r
 \r
       viewport.setGlobalColourScheme(cs);\r
     }\r
     else if (cs instanceof ResidueColourScheme)\r
     {\r
-      ( (ResidueColourScheme) cs).setThreshold(0);\r
+      ( (ResidueColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
     }\r
 \r
     if (viewport.getConservationSelected())\r
@@ -844,7 +885,7 @@ public class AlignFrame
         {\r
           if (sg.cs instanceof ResidueColourScheme)\r
           {\r
-            ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+            ( (ResidueColourScheme) sg.cs).setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
           }\r
 \r
           sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
@@ -873,6 +914,8 @@ public class AlignFrame
       }\r
     }\r
 \r
+    updateCSConsensus();\r
+\r
     if (alignPanel.getOverviewPanel() != null)\r
     {\r
       alignPanel.getOverviewPanel().updateOverviewImage();\r
@@ -881,6 +924,12 @@ public class AlignFrame
     alignPanel.repaint();\r
   }\r
 \r
+  public void updateCSConsensus()\r
+  {\r
+    //Colour schemes must have their consensus updated\r
+\r
+  }\r
+\r
   protected void modifyPID_actionPerformed(ActionEvent e)\r
   {\r
     if (viewport.getAbovePIDThreshold())\r
@@ -1053,7 +1102,21 @@ public class AlignFrame
     //are the sequences aligned?\r
     if (!viewport.alignment.isAligned())\r
     {\r
-      return;\r
+      SequenceI current;\r
+      int Width = viewport.getAlignment().getWidth();\r
+\r
+      for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+           i++)\r
+      {\r
+        current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+        if (current.getLength() < Width)\r
+        {\r
+          current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+        }\r
+      }\r
+      alignPanel.repaint();\r
+\r
     }\r
 \r
     final TreePanel tp;\r
@@ -1119,7 +1182,7 @@ public class AlignFrame
         int y = 5, x = 7;\r
         g.setColor(Color.black);\r
         g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
-        g.drawString("JalView - Release 2.0", 200, y += fh);\r
+        g.drawString("JalView - Release 2.02", 200, y += fh);\r
         g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
         g.drawString("Authors:  Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
                      x, y += fh * 2);\r