X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=d47d89d84ac30ad309ef1cd298e1006341bbf8a8;hb=3596077c79b7aa2051b9aaa978481004b513101c;hp=536d178c160e19f685ddfcc61815c3c191a7d98d;hpb=1ab3860add27db695e8471783bf775ecff1fdae9;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 536d178..d47d89d 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -27,6 +27,8 @@ import java.awt.event.*;
 
 import javax.swing.*;
 
+import java.util.Vector;
+
 
 /**
  * DOCUMENT ME!
@@ -65,10 +67,13 @@ public class SeqPanel extends JPanel implements MouseListener,
     SequenceGroup stretchGroup = null;
     boolean remove = false;
 
+    Point lastMousePress;
     boolean mouseWheelPressed = false;
     StringBuffer keyboardNo1;
     StringBuffer keyboardNo2;
 
+    java.net.URL linkImageURL;
+
     /**
      * Creates a new SeqPanel object.
      *
@@ -77,6 +82,7 @@ public class SeqPanel extends JPanel implements MouseListener,
      */
     public SeqPanel(AlignViewport avp, AlignmentPanel p)
     {
+        linkImageURL = getClass().getResource("/images/link.gif");
         ToolTipManager.sharedInstance().registerComponent(this);
         ToolTipManager.sharedInstance().setInitialDelay(0);
         ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -141,7 +147,6 @@ public class SeqPanel extends JPanel implements MouseListener,
 
    int findSeq(MouseEvent evt)
    {
-
      int seq = 0;
      int y = evt.getY();
 
@@ -156,16 +161,41 @@ public class SeqPanel extends JPanel implements MouseListener,
 
          y -= hgap;
 
-       seq = ( (y % cHeight) / av.getCharHeight());
+       seq = Math.min( (y % cHeight) / av.getCharHeight(),
+                       av.alignment.getHeight() -1);
      }
      else
      {
-       seq = (y / av.getCharHeight()) + av.getStartSeq();
+       seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+                       av.alignment.getHeight() -1);
      }
 
      return seq;
    }
 
+   Vector getAllFeaturesAtRes(SequenceI seq, int res)
+   {
+     Vector allFeatures = new Vector();
+     int index = 0;
+     if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null)
+     {
+       while (index < seq.getSequenceFeatures().length)
+       {
+         SequenceFeature sf = seq.getSequenceFeatures()[index];
+         if (sf.getBegin() <= res &&
+             sf.getEnd() >= res)
+         {
+           if (av.featuresDisplayed.containsKey(sf.getType()))
+           {
+             allFeatures.addElement(sf);
+           }
+         }
+         index++;
+       }
+     }
+     return allFeatures;
+  }
+
    void endEditing()
    {
      startseq = -1;
@@ -235,25 +265,34 @@ public class SeqPanel extends JPanel implements MouseListener,
 
 
       endEditing();
-      while (seqCanvas.cursorY < av.startSeq)
+      if(av.wrapAlignment)
       {
-        ap.scrollUp(true);
+        ap.scrollToWrappedVisible(seqCanvas.cursorX);
       }
-      while (seqCanvas.cursorY + 1 > av.endSeq)
-      {
-        ap.scrollUp(false);
-      }
-      while (seqCanvas.cursorX < av.startRes)
-      {
-        if(!ap.scrollRight(false))
-          break;
-      }
-      while (seqCanvas.cursorX > av.endRes)
+      else
       {
-        if(!ap.scrollRight(true))
-          break;
+        while (seqCanvas.cursorY < av.startSeq)
+        {
+          ap.scrollUp(true);
+        }
+        while (seqCanvas.cursorY + 1 > av.endSeq)
+        {
+          ap.scrollUp(false);
+        }
+        if (!av.wrapAlignment)
+        {
+          while (seqCanvas.cursorX < av.startRes)
+          {
+            if (!ap.scrollRight(false))
+              break;
+          }
+          while (seqCanvas.cursorX > av.endRes)
+          {
+            if (!ap.scrollRight(true))
+              break;
+          }
+        }
       }
-
       setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
                        seqCanvas.cursorX, seqCanvas.cursorY);
 
@@ -270,7 +309,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         SequenceGroup sg = av.selectionGroup;
         //Find the top and bottom of this group
         int min = av.alignment.getHeight(), max = 0;
-        for(int i=0; i<sg.getSize(); i++)
+        for(int i=0; i<sg.getSize(false); i++)
         {
           int index = av.alignment.findIndex( sg.getSequenceAt(i) );
           if(index > max)
@@ -306,7 +345,7 @@ public class SeqPanel extends JPanel implements MouseListener,
         else
         {
           // Now add any sequences between min and max
-          sg.sequences.clear();
+          sg.getSequences(false).clear();
           for (int i = min; i < max; i++)
           {
             sg.addSequence(av.alignment.getSequenceAt(i), false);
@@ -387,7 +426,6 @@ public class SeqPanel extends JPanel implements MouseListener,
 
        editOccurred();
 
-       endEditing();
        ap.repaint();
     }
 
@@ -400,6 +438,8 @@ public class SeqPanel extends JPanel implements MouseListener,
      */
     public void mousePressed(MouseEvent evt)
     {
+      lastMousePress = evt.getPoint();
+
       if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
       {
         mouseWheelPressed = true;
@@ -489,6 +529,7 @@ public class SeqPanel extends JPanel implements MouseListener,
             if(features!=null)
             {
               StringBuffer sbuffer = new StringBuffer("<html>");
+              StringBuffer seqSpecific =  new StringBuffer();
 
               for (int i = 0; i < features.length; i++)
               {
@@ -510,30 +551,46 @@ public class SeqPanel extends JPanel implements MouseListener,
                         sbuffer.append("<br>");
                       sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
                                      features[i].getEnd());
+                      if (features[i].links != null)
+                      sbuffer.append(" <img src=\"" + linkImageURL + "\">");
                     }
                   }
                   else
                   {
                     if (sbuffer.length() > 6)
                       sbuffer.append("<br>");
-                    if(features[i].featureGroup!=null)
-                      sbuffer.append(features[i].featureGroup+";");
 
-                    sbuffer.append(features[i].getType());
+                    sbuffer.append(features[i].getType() + " " +
+                                   features[i].begin);
+                    if (features[i].begin != features[i].end)
+                      sbuffer.append(" " + features[i].end);
 
                     if (features[i].getDescription() != null
                         && !features[i].description.equals(features[i].getType()))
                       sbuffer.append("; " + features[i].getDescription());
 
-                    if (features[i].getStatus() != null && features[i].getStatus().length()>0)
+                    if (features[i].getValue("status") != null)
                     {
-                      sbuffer.append("; (" + features[i].getStatus() + ")");
+                      sbuffer.append("; (" + features[i].getValue("status") + ")");
                     }
+                    if (features[i].links != null)
+                      sbuffer.append(" <img src=\"" + linkImageURL + "\">");
+
                   }
                 }
+                else if(features[i].begin==0 && features[i].end==0)
+                {
+                  // seqSpecific.append(features[i].featureGroup+": "
+                  //                   + features[i].getType()+" "
+                   //                   +features[i].getDescription()+"<br>");
 
+                }
               }
 
+              if(seqSpecific.length()>0)
+                seqSpecific.setLength(seqSpecific.length()-4);
+
+              sbuffer.append(seqSpecific);
               sbuffer.append("</html>");
               if(sbuffer.length()==13) // <html></html>
                 setToolTipText("");
@@ -585,6 +642,54 @@ public class SeqPanel extends JPanel implements MouseListener,
      */
     public void mouseDragged(MouseEvent evt)
     {
+      if (mouseWheelPressed)
+      {
+        int oldWidth = av.charWidth;
+
+        //Which is bigger, left-right or up-down?
+        if (Math.abs(evt.getY() - lastMousePress.getY())
+            > Math.abs(evt.getX() - lastMousePress.getX()))
+        {
+          int fontSize = av.font.getSize();
+
+          if (evt.getY() < lastMousePress.getY())
+          {
+            fontSize--;
+          }
+          else if (evt.getY() > lastMousePress.getY())
+          {
+            fontSize++;
+          }
+
+          if(fontSize<1)
+            fontSize = 1;
+
+          av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+          av.charWidth = oldWidth;
+          ap.fontChanged();
+        }
+        else
+        {
+          if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+          {
+            av.charWidth--;
+          }
+          else if (evt.getX() > lastMousePress.getX())
+          {
+            av.charWidth++;
+          }
+
+          ap.repaint();
+        }
+
+        FontMetrics fm = getFontMetrics(av.getFont());
+        av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+
+        lastMousePress = evt.getPoint();
+
+        return;
+      }
+
       if (!editingSeqs)
       {
         doMouseDraggedDefineMode(evt);
@@ -624,25 +729,29 @@ public class SeqPanel extends JPanel implements MouseListener,
       boolean fixedColumns = false;
       SequenceGroup sg = av.getSelectionGroup();
 
-      if(groupEditing && sg==null)
-        return;
 
         if (!groupEditing && av.hasHiddenRows)
         {
-          //This needs to check all the sequences in a group edit,m
-          // not just the startseq
           if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
           {
             groupEditing = true;
           }
         }
 
+        //No group, but the sequence may represent a group
+        if (groupEditing
+            && sg == null
+            && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
+        {
+          groupEditing = false;
+        }
+
         SequenceI seq = av.alignment.getSequenceAt(startseq);
         StringBuffer message = new StringBuffer();
         if (groupEditing)
            message.append("Edit group:");
         else
-            message.append("Edit sequence: "+seq.getName());
+           message.append("Edit sequence: "+seq.getName());
 
        if(insertGap)
          message.append(" insert ");
@@ -655,10 +764,19 @@ public class SeqPanel extends JPanel implements MouseListener,
 
         //Are we editing within a selection group?
         if (groupEditing
-            || (sg != null && sg.sequences.contains(seq)))
+            || (sg != null && sg.getSequences(true).contains(seq)))
         {
           fixedColumns = true;
 
+          //sg might be null as the user may only see 1 sequence,
+          //but the sequence represents a group
+          if (sg == null)
+          {
+            sg = new SequenceGroup(null, null, false, false, false, 0,
+                                   av.alignment.getWidth()-1);
+            sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+          }
+
           fixedLeft = sg.getStartRes();
           fixedRight = sg.getEndRes();
 
@@ -684,64 +802,46 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
 
 
-
-        if(av.hasHiddenColumns)
-        {
-          fixedColumns = true;
-          int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
-          int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
-
-          if(    ( insertGap && startres>y1 && lastres<y1)
-              || (!insertGap && startres<y2 && lastres>y2) )
-          {
-            endEditing();
-            return;
-          }
-
-          if(fixedRight<y2 && fixedRight==-1 && y2!=startres)
-            fixedRight = y2 -1;
-          if(y1>fixedLeft && fixedLeft==-1)
-            fixedLeft = y1;
-        }
-
-        if (groupEditing)
+        if(av.hasHiddenColumns )
         {
+            fixedColumns = true;
+            int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+            int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
 
-          /*if (av.hasHiddenRows)
-          {
-            //sg might be null as the user may only see 1 sequence
-            if (sg == null)
+            if ( (insertGap && startres > y1 && lastres < y1)
+                || (!insertGap && startres < y2 && lastres > y2))
             {
-              sg = new SequenceGroup();
-              sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+              endEditing();
+              return;
             }
 
-            SequenceGroup tmp = new SequenceGroup();
-
-            //Do any of the sequences have hidden associates?
-            for (int s = 0; s < sg.getSize(); s++)
+            //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+            //Selection spans a hidden region
+            if(fixedLeft<y1 && (fixedRight>y2 || fixedRight==-1))
             {
-              seq = sg.getSequenceAt(s);
-              tmp.addSequence(seq, false);
-              if (seq.getHiddenSequences() != null)
+              if(startres>=y2)
               {
-                for (int h = 0; h < seq.getHiddenSequences().getSize(); h++)
-                  tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h),
-                                  false);
+                fixedLeft = y2;
               }
+              else
+              {
+               fixedRight = y2 - 1;
+             }
             }
-
-            sg = tmp;
-          }*/
-          // int blankColumn = -1;
+        }
 
 
+        if (groupEditing)
+        {
           // drag to right
           if (insertGap)
           {
               //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() + 1 == av.alignment.getWidth())
+              if(   sg.getStartRes() == 0
+                    && sg.getEndRes() == fixedRight
+                    && sg.getEndRes() == av.alignment.getWidth()-1
+                 )
               {
                 sg.setEndRes(av.alignment.getWidth() + startres - lastres);
                 fixedRight = sg.getEndRes();
@@ -756,9 +856,9 @@ public class SeqPanel extends JPanel implements MouseListener,
                  fixedRight--)
             {
               blank = true;
-              for (int s = 0; s < sg.getSize(); s++)
+              for (int s = 0; s < sg.getSize(true); s++)
               {
-                seq = sg.getSequenceAt(s);
+                seq = (SequenceI)sg.getSequences(true).elementAt(s);
                 for (int j = 0; j < startres - lastres; j++)
                 {
                   if (!jalview.util.Comparison.isGap(
@@ -775,12 +875,26 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             if (!blank)
             {
-              if(sg.getSize() == av.alignment.getHeight())
+              if(sg.getSize(false) == av.alignment.getHeight()  )
               {
+                if((av.hasHiddenColumns
+                    && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
+                {
+                  endEditing();
+                  return;
+                }
+
+                int alWidth = av.alignment.getWidth();
+                if(av.hasHiddenRows)
+                {
+                  int hwidth = av.alignment.getHiddenSequences().getWidth();
+                  if(hwidth>alWidth)
+                    alWidth = hwidth;
+                }
                 //We can still insert gaps if the selectionGroup
                 //contains all the sequences
-                sg.setEndRes(sg.getEndRes()+1+startres-lastres);
-                fixedRight = av.alignment.getWidth()+startres-lastres;
+                sg.setEndRes(sg.getEndRes()+startres-lastres);
+                fixedRight = alWidth+startres-lastres;
               }
               else
               {
@@ -797,9 +911,9 @@ public class SeqPanel extends JPanel implements MouseListener,
             /// Are we able to delete?
             // ie are all columns blank?
 
-            for (int s = 0; s < sg.getSize(); s++)
+            for (int s = 0; s < sg.getSize(true); s++)
             {
-              seq = sg.getSequenceAt(s);
+              seq = (SequenceI)sg.getSequences(true).elementAt(s);
 
               for (int j = startres; j < lastres; j++)
               {
@@ -820,9 +934,9 @@ public class SeqPanel extends JPanel implements MouseListener,
           }
 
 
-          for (int i = 0; i < sg.getSize(); i++)
+          for (int i = 0; i < sg.getSize(true); i++)
           {
-            seq = sg.getSequenceAt(i);
+            seq = (SequenceI) sg.getSequences(true).elementAt(i);
 
             if (insertGap)
             {
@@ -863,17 +977,6 @@ public class SeqPanel extends JPanel implements MouseListener,
             {
               if (fixedColumns && fixedRight != -1)
               {
-                if (sg.getStartRes() == 0
-                    && sg.getEndRes() + 1 == av.alignment.getWidth()
-                    && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight)))
-                {
-                  //Single sequence edit, whole sequence selected,
-                  //extend the selection group
-                  sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres);
-                  fixedColumns = false;
-                  insertChar(j, seq);
-                }
-                else
                   insertChar(j, seq, fixedRight);
               }
               else
@@ -930,6 +1033,9 @@ public class SeqPanel extends JPanel implements MouseListener,
 
       if (blankColumn <= j)
       {
+        System.out.println("END HERE "+seq.getName()+" "+seq.getLength()+" "+j+" "
+            +blankColumn+" "+fixedColumn);
+        blankColumn = fixedColumn;
         endEditing();
         return;
       }
@@ -1020,7 +1126,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     public void mouseWheelMoved(MouseWheelEvent e)
     {
       e.consume();
-      if (mouseWheelPressed)
+     /* if (mouseWheelPressed)
       {
         Font font = av.getFont();
         int fontSize = font.getSize();
@@ -1029,10 +1135,13 @@ public class SeqPanel extends JPanel implements MouseListener,
         else if (fontSize > 1)
           fontSize--;
 
+
+
         av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
+
         ap.fontChanged();
       }
-      else
+      else*/
       {
         if (e.getWheelRotation() > 0)
           ap.scrollUp(false);
@@ -1082,7 +1191,7 @@ public class SeqPanel extends JPanel implements MouseListener,
               "Cannot edit annotations in wrapped view.",
               "Wrapped view - no edit",
               JOptionPane.WARNING_MESSAGE);
-        return;
+          return;
       }
 
       if(seq<0 || res<0)
@@ -1111,7 +1220,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                 stretchGroup = null;
             }
         }
-        else if (!stretchGroup.sequences.contains(sequence) ||
+        else if (!stretchGroup.getSequences(false).contains(sequence) ||
                 (stretchGroup.getStartRes() > res) ||
                 (stretchGroup.getEndRes() < res))
         {
@@ -1127,12 +1236,13 @@ public class SeqPanel extends JPanel implements MouseListener,
                             (allGroups[i].getEndRes() >= res))
                     {
                         stretchGroup = allGroups[i];
-                        av.setSelectionGroup(stretchGroup);
-
                         break;
                     }
                 }
             }
+
+            av.setSelectionGroup(stretchGroup);
+
         }
 
         if (av.cursorMode)
@@ -1144,49 +1254,65 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
 
 
-        if (stretchGroup == null)
+        if (javax.swing.SwingUtilities.isRightMouseButton(evt))
         {
-            // define a new group here
-            SequenceGroup sg = new SequenceGroup();
-            sg.setStartRes(res);
-            sg.setEndRes(res);
-            sg.addSequence(sequence, false);
-            av.setSelectionGroup(sg);
-            stretchGroup = sg;
-
-            if (av.getConservationSelected())
+          Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
+                                                  sequence.findPosition(res));
+          Vector links = new Vector();
+            for (int i = 0; i < allFeatures.size(); i++)
             {
-                SliderPanel.setConservationSlider(ap,
-                    av.getGlobalColourScheme(), "Background");
+              SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
+              if (sf.links != null)
+              {
+                for (int j = 0; j < sf.links.size(); j++)
+                {
+                  links.addElement(sf.links.elementAt(j));
+                }
+              }
             }
 
-            if (av.getAbovePIDThreshold())
-            {
-                SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                    "Background");
-            }
-        }
-        else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
-        {
-            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
+            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
             pop.show(this, evt.getX(), evt.getY());
 
-            // edit the properties of existing group
         }
-
-        if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
+        else if (stretchGroup == null)
         {
+          //Only if left mouse button do we want to change group sizes
+
+          // define a new group here
+          SequenceGroup sg = new SequenceGroup();
+          sg.setStartRes(res);
+          sg.setEndRes(res);
+          sg.addSequence(sequence, false);
+          av.setSelectionGroup(sg);
+          stretchGroup = sg;
+
+          if (av.getConservationSelected())
+          {
+            SliderPanel.setConservationSlider(ap,
+                                              av.getGlobalColourScheme(),
+                                              "Background");
+          }
+
+          if (av.getAbovePIDThreshold())
+          {
+            SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                                           "Background");
+          }
+          if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
+          {
             // Edit end res position of selected group
             changeEndRes = true;
-        }
-        else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
-        {
+          }
+          else if ( (stretchGroup != null) &&
+                   (stretchGroup.getStartRes() == res))
+          {
             // Edit end res position of selected group
             changeStartRes = true;
+          }
+          stretchGroup.getWidth();
         }
 
-        stretchGroup.getWidth();
-
         seqCanvas.repaint();
     }
 
@@ -1207,8 +1333,8 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           if (stretchGroup.cs instanceof ClustalxColourScheme)
           {
-            ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
-                sequences,
+            ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+                stretchGroup.getSequences(true),
                 stretchGroup.getWidth());
           }
 
@@ -1248,11 +1374,6 @@ public class SeqPanel extends JPanel implements MouseListener,
             return;
        }
 
-
-        if(y > av.alignment.getHeight())
-        {
-          y = av.alignment.getHeight() -1;
-        }
         if(res> av.alignment.getWidth())
         {
           res = av.alignment.getWidth()-1;
@@ -1314,7 +1435,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
             Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-            if (stretchGroup.sequences.contains(nextSeq))
+            if (stretchGroup.getSequences(false).contains(nextSeq))
             {
                 stretchGroup.deleteSequence(seq, false);
             }