X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=13527d05d795dd9108d0a3011ae5f2bce4246483;hb=0b9d0f8eba1cec46c0b31fdd402a826e26244ff5;hp=ca5d7f7be2a2ba74bf6cddd90cc029cb0aeb28e9;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ca5d7f7..13527d0 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -18,6 +18,7 @@
 package jalview.gui;
 
 import java.util.*;
+import java.util.List;
 
 import java.awt.*;
 import java.awt.event.*;
@@ -176,7 +177,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       res = (x / av.getCharWidth()) + av.getStartRes();
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       res = av.getColumnSelection().adjustForHiddenColumns(res);
     }
@@ -204,12 +205,12 @@ public class SeqPanel extends JPanel implements MouseListener,
       y -= hgap;
 
       seq = Math.min((y % cHeight) / av.getCharHeight(),
-              av.alignment.getHeight() - 1);
+              av.getAlignment().getHeight() - 1);
     }
     else
     {
       seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
-              av.alignment.getHeight() - 1);
+              av.getAlignment().getHeight() - 1);
     }
 
     return seq;
@@ -308,19 +309,19 @@ public class SeqPanel extends JPanel implements MouseListener,
   {
     seqCanvas.cursorX += dx;
     seqCanvas.cursorY += dy;
-    if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+    if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
     {
       int original = seqCanvas.cursorX - dx;
-      int maxWidth = av.alignment.getWidth();
+      int maxWidth = av.getAlignment().getWidth();
 
-      while (!av.colSel.isVisible(seqCanvas.cursorX)
+      while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
               && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
       {
         seqCanvas.cursorX += dx;
       }
 
       if (seqCanvas.cursorX >= maxWidth
-              || !av.colSel.isVisible(seqCanvas.cursorX))
+              || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
       {
         seqCanvas.cursorX = original;
       }
@@ -335,18 +336,18 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       seqCanvas.cursorX = 0;
     }
-    else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+    else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
     {
-      seqCanvas.cursorX = av.alignment.getWidth() - 1;
+      seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
     }
 
     if (seqCanvas.cursorY < 0)
     {
       seqCanvas.cursorY = 0;
     }
-    else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+    else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
     {
-      seqCanvas.cursorY = av.alignment.getHeight() - 1;
+      seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
     }
 
     endEditing();
@@ -366,7 +367,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
       if (!av.wrapAlignment)
       {
-        while (seqCanvas.cursorX < av.colSel
+        while (seqCanvas.cursorX < av.getColumnSelection()
                 .adjustForHiddenColumns(av.startRes))
         {
           if (!ap.scrollRight(false))
@@ -374,7 +375,7 @@ public class SeqPanel extends JPanel implements MouseListener,
             break;
           }
         }
-        while (seqCanvas.cursorX > av.colSel
+        while (seqCanvas.cursorX > av.getColumnSelection()
                 .adjustForHiddenColumns(av.endRes))
         {
           if (!ap.scrollRight(true))
@@ -384,7 +385,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
       }
     }
-    setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+    setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
 
     seqCanvas.repaint();
@@ -397,12 +398,12 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (av.getSelectionGroup() != null)
     {
-      SequenceGroup sg = av.selectionGroup;
+      SequenceGroup sg = av.getSelectionGroup();
       // Find the top and bottom of this group
-      int min = av.alignment.getHeight(), max = 0;
+      int min = av.getAlignment().getHeight(), max = 0;
       for (int i = 0; i < sg.getSize(); i++)
       {
-        int index = av.alignment.findIndex(sg.getSequenceAt(i));
+        int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
         if (index > max)
         {
           max = index;
@@ -447,7 +448,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         sg.getSequences(null).clear();
         for (int i = min; i < max; i++)
         {
-          sg.addSequence(av.alignment.getSequenceAt(i), false);
+          sg.addSequence(av.getAlignment().getSequenceAt(i), false);
         }
       }
     }
@@ -470,7 +471,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     groupEditing = group;
     startseq = seqCanvas.cursorY;
     lastres = seqCanvas.cursorX;
-    editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
+    editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
     endEditing();
   }
 
@@ -479,9 +480,17 @@ public class SeqPanel extends JPanel implements MouseListener,
     groupEditing = group;
     startseq = seqCanvas.cursorY;
     lastres = seqCanvas.cursorX + getKeyboardNo1();
-    editSequence(false, seqCanvas.cursorX);
+    editSequence(false, false, seqCanvas.cursorX);
     endEditing();
   }
+  
+  void insertNucAtCursor(boolean group,String nuc){
+	  groupEditing = group;
+	    startseq = seqCanvas.cursorY;
+	    lastres = seqCanvas.cursorX;
+	    editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
+	    endEditing();
+  }
 
   void numberPressed(char value)
   {
@@ -665,7 +674,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     tooltipText.setLength(6); // Cuts the buffer back to <html>
 
-    SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+    SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
     if (groups != null)
     {
       for (int g = 0; g < groups.length; g++)
@@ -904,7 +913,7 @@ public class SeqPanel extends JPanel implements MouseListener,
             + sequence.getName());
 
     Object obj = null;
-    if (av.alignment.isNucleotide())
+    if (av.getAlignment().isNucleotide())
     {
       obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
               + "");
@@ -1013,11 +1022,11 @@ public class SeqPanel extends JPanel implements MouseListener,
     if ((res < av.getAlignment().getWidth()) && (res < lastres))
     {
       // dragLeft, delete gap
-      editSequence(false, res);
+      editSequence(false, false,res);
     }
     else
     {
-      editSequence(true, res);
+      editSequence(true, false,res);
     }
 
     mouseDragging = true;
@@ -1027,22 +1036,22 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
   }
 
-  synchronized void editSequence(boolean insertGap, int startres)
+  //TODO: Make it more clever than many booleans
+  synchronized void editSequence(boolean insertGap, boolean editSeq, int startres)
   {
     int fixedLeft = -1;
     int fixedRight = -1;
     boolean fixedColumns = false;
     SequenceGroup sg = av.getSelectionGroup();
 
-    SequenceI seq = av.alignment.getSequenceAt(startseq);
+    SequenceI seq = av.getAlignment().getSequenceAt(startseq);
 
     // No group, but the sequence may represent a group
-    if (!groupEditing && av.hasHiddenRows)
+    if (!groupEditing && av.hasHiddenRows())
     {
-      if (av.hiddenRepSequences != null
-              && av.hiddenRepSequences.containsKey(seq))
+      if (av.isHiddenRepSequence(seq))
       {
-        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+        sg = av.getRepresentedSequences(seq);
         groupEditing = true;
       }
     }
@@ -1084,7 +1093,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     // Are we editing within a selection group?
     if (groupEditing
-            || (sg != null && sg.getSequences(av.hiddenRepSequences)
+            || (sg != null && sg.getSequences(av.getHiddenRepSequences())
                     .contains(seq)))
     {
       fixedColumns = true;
@@ -1093,13 +1102,12 @@ public class SeqPanel extends JPanel implements MouseListener,
       // but the sequence represents a group
       if (sg == null)
       {
-        if (av.hiddenRepSequences == null
-                || !av.hiddenRepSequences.containsKey(seq))
+        if (!av.isHiddenRepSequence(seq))
         {
           endEditing();
           return;
         }
-        sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+        sg = av.getRepresentedSequences(seq);
       }
 
       fixedLeft = sg.getStartRes();
@@ -1126,7 +1134,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       }
     }
 
-    if (av.hasHiddenColumns)
+    if (av.hasHiddenColumns())
     {
       fixedColumns = true;
       int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
@@ -1156,12 +1164,12 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (groupEditing)
     {
-      Vector vseqs = sg.getSequences(av.hiddenRepSequences);
+      List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
       int g, groupSize = vseqs.size();
       SequenceI[] groupSeqs = new SequenceI[groupSize];
       for (g = 0; g < groupSeqs.length; g++)
       {
-        groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+        groupSeqs[g] = (SequenceI) vseqs.get(g);
       }
 
       // drag to right
@@ -1170,9 +1178,9 @@ public class SeqPanel extends JPanel implements MouseListener,
         // If the user has selected the whole sequence, and is dragging to
         // the right, we can still extend the alignment and selectionGroup
         if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
-                && sg.getEndRes() == av.alignment.getWidth() - 1)
+                && sg.getEndRes() == av.getAlignment().getWidth() - 1)
         {
-          sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+          sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
           fixedRight = sg.getEndRes();
         }
 
@@ -1204,19 +1212,19 @@ public class SeqPanel extends JPanel implements MouseListener,
 
         if (!blank)
         {
-          if (sg.getSize() == av.alignment.getHeight())
+          if (sg.getSize() == av.getAlignment().getHeight())
           {
-            if ((av.hasHiddenColumns && startres < av.getColumnSelection()
+            if ((av.hasHiddenColumns() && startres < av.getColumnSelection()
                     .getHiddenBoundaryRight(startres)))
             {
               endEditing();
               return;
             }
 
-            int alWidth = av.alignment.getWidth();
-            if (av.hasHiddenRows)
+            int alWidth = av.getAlignment().getWidth();
+            if (av.hasHiddenRows())
             {
-              int hwidth = av.alignment.getHiddenSequences().getWidth();
+              int hwidth = av.getAlignment().getHiddenSequences().getWidth();
               if (hwidth > alWidth)
               {
                 alWidth = hwidth;
@@ -1273,7 +1281,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         else
         {
           editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
-                  startres, startres - lastres, av.alignment, true);
+                  startres, startres - lastres, av.getAlignment(), true);
         }
       }
       else
@@ -1289,7 +1297,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         else
         {
           editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
-                  startres, lastres - startres, av.alignment, true);
+                  startres, lastres - startres, av.getAlignment(), true);
         }
 
       }
@@ -1311,11 +1319,12 @@ public class SeqPanel extends JPanel implements MouseListener,
         else
         {
           editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
-          { seq }, lastres, startres - lastres, av.alignment, true);
-        }
+          { seq }, lastres, startres - lastres, av.getAlignment(), true);
+         }
       }
       else
       {
+    	if(!editSeq){
         // dragging to the left
         if (fixedColumns && fixedRight != -1)
         {
@@ -1346,9 +1355,24 @@ public class SeqPanel extends JPanel implements MouseListener,
           if (max > 0)
           {
             editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
-            { seq }, startres, max, av.alignment, true);
+            { seq }, startres, max, av.getAlignment(), true);
           }
         }
+    	}else{//insertGap==false AND editSeq==TRUE;
+    		if (fixedColumns && fixedRight != -1)
+            {
+              for (int j = lastres; j < startres; j++)
+              {
+                insertChar(j, new SequenceI[]
+                { seq }, fixedRight);
+              }
+              }
+            else
+            {
+              editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
+              { seq }, lastres, startres - lastres, av.getAlignment(), true);
+             }
+    	}
       }
     }
 
@@ -1382,9 +1406,9 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
 
     editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
-            av.alignment, true);
+            av.getAlignment(), true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
+    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(),
             true);
 
   }
@@ -1392,11 +1416,11 @@ public class SeqPanel extends JPanel implements MouseListener,
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
+    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(),
             true);
 
     editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
-            av.alignment, true);
+            av.getAlignment(), true);
   }
 
   /**
@@ -1441,7 +1465,7 @@ public class SeqPanel extends JPanel implements MouseListener,
   public void mouseClicked(MouseEvent evt)
   {
     SequenceGroup sg = null;
-    SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+    SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
     if (evt.getClickCount() > 1)
     {
       sg = av.getSelectionGroup();
@@ -1500,7 +1524,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     startWrapBlock = wrappedBlock;
 
-    if (av.wrapAlignment && seq > av.alignment.getHeight())
+    if (av.wrapAlignment && seq > av.getAlignment().getHeight())
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
               "Cannot edit annotations in wrapped view.",
@@ -1524,7 +1548,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (stretchGroup == null)
     {
-      stretchGroup = av.alignment.findGroup(sequence);
+      stretchGroup = av.getAlignment().findGroup(sequence);
 
       if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
               && (res < stretchGroup.getEndRes()))
@@ -1542,7 +1566,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       stretchGroup = null;
 
-      SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+      SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
 
       if (allGroups != null)
       {
@@ -1650,9 +1674,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-        ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
-                stretchGroup.getSequences(av.hiddenRepSequences),
-                stretchGroup.getWidth());
+        ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged(
+                stretchGroup,av.getHiddenRepSequences());
       }
 
       if (stretchGroup.cs.conservationApplied())
@@ -1696,9 +1719,9 @@ public class SeqPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (res >= av.alignment.getWidth())
+    if (res >= av.getAlignment().getWidth())
     {
-      res = av.alignment.getWidth() - 1;
+      res = av.getAlignment().getWidth() - 1;
     }
 
     if (stretchGroup.getEndRes() == res)
@@ -1743,7 +1766,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       dragDirection = -1;
     }
 
-    while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+    while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight()))
     {
       // This routine ensures we don't skip any sequences, as the
       // selection is quite slow.
@@ -1848,7 +1871,7 @@ public class SeqPanel extends JPanel implements MouseListener,
           }
 
           if (mouseDragging && (evt.getY() >= getHeight())
-                  && (av.alignment.getHeight() > av.getEndSeq()))
+                  && (av.getAlignment().getHeight() > av.getEndSeq()))
           {
             running = ap.scrollUp(false);
           }
@@ -1901,15 +1924,15 @@ public class SeqPanel extends JPanel implements MouseListener,
       SequenceGroup sgroup = null;
       if (seqsel != null && seqsel.getSize()>0)
       {
-        if (av.alignment == null)
+        if (av.getAlignment() == null)
         {
           jalview.bin.Cache.log.warn("alignviewport av SeqSetId="
                   + av.getSequenceSetId() + " ViewId=" + av.getViewId()
                   + " 's alignment is NULL! returning immediatly.");
           return;
         }
-        sgroup = seqsel.intersect(av.alignment,
-                (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+        sgroup = seqsel.intersect(av.getAlignment(),
+                (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
         if ((sgroup == null || sgroup.getSize() == 0)
                 || (colsel == null || colsel.size() == 0))
         {
@@ -1934,29 +1957,29 @@ public class SeqPanel extends JPanel implements MouseListener,
       // so import the new colsel.
       if (colsel == null || colsel.size() == 0)
       {
-        if (av.colSel != null)
+        if (av.getColumnSelection() != null)
         {
-          av.colSel.clear();
+          av.getColumnSelection().clear();
           repaint=true;
         }
       }
       else
       {
         // TODO: shift colSel according to the intersecting sequences
-        if (av.colSel == null)
+        if (av.getColumnSelection() == null)
         {
-          av.colSel = new ColumnSelection(colsel);
+          av.setColumnSelection(new ColumnSelection(colsel));
         }
         else
         {
-          av.colSel.setElementsFrom(colsel);
+          av.getColumnSelection().setElementsFrom(colsel);
         }
       }
       av.isColSelChanged(true);
       repaint = true;
     }
-    if (copycolsel && av.hasHiddenColumns
-            && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+    if (copycolsel && av.hasHiddenColumns()
+            && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null))
     {
       System.err.println("Bad things");
     }