X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=d45759343751073e7574c9aca7e9939bf29b81ee;hb=af2fbc5499bfc4764ad69e1abaa35eee4dd04817;hp=3f49cc49ca923ab2972778efa65f26fc3e9a3c15;hpb=99f3f01792321efb671ac7ad946efffc3a3319a4;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 3f49cc4..d457593 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!
@@ -65,7 +67,12 @@ 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.
@@ -75,6 +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);
@@ -164,6 +172,29 @@ public class SeqPanel extends JPanel implements MouseListener,
      return seq;
    }
 
+   Vector getAllFeaturesAtRes(SequenceI seq, int res)
+   {
+     Vector allFeatures = new Vector();
+     int index = 0;
+     if(seq.getSequenceFeatures()!=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;
@@ -171,35 +202,99 @@ public class SeqPanel extends JPanel implements MouseListener,
      seqEditOccurred = false;
      editingSeqs = false;
      groupEditing = false;
-     keyboardGaps = null;
+     keyboardNo1 = null;
+     keyboardNo2 = null;
+    }
+
+    void setCursorRow()
+    {
+      seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1;
+      scrollToVisible();
     }
 
+    void setCursorColumn()
+    {
+      seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1;
+      scrollToVisible();
+    }
+
+    void setCursorRowAndColumn()
+    {
+      if(keyboardNo2==null)
+      {
+        keyboardNo2 = new StringBuffer();
+      }
+      else
+      {
+        seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
+        seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
+        scrollToVisible();
+      }
+    }
+
+    void setCursorPosition()
+    {
+      SequenceI sequence =
+          (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+      seqCanvas.cursorX = sequence.findIndex(
+          getKeyboardNo(keyboardNo1)-1
+          );
+      scrollToVisible();
+    }
 
     void moveCursor(int dx, int dy)
     {
       seqCanvas.cursorX += dx;
       seqCanvas.cursorY += dy;
+      scrollToVisible();
+    }
 
-      if(seqCanvas.cursorX<0)
+    void scrollToVisible()
+    {
+      if (seqCanvas.cursorX < 0)
         seqCanvas.cursorX = 0;
-      else if(seqCanvas.cursorX>av.alignment.getWidth()-1)
-        seqCanvas.cursorX = av.alignment.getWidth()-1;
-      if(seqCanvas.cursorX<av.startRes)
-        ap.scrollRight(false);
-      else if(seqCanvas.cursorX>av.endRes)
-        ap.scrollRight(true);
-
-      if(seqCanvas.cursorY<0)
-        seqCanvas.cursorY=0;
-      else if(seqCanvas.cursorY>av.alignment.getHeight()-1)
-        seqCanvas.cursorY = av.alignment.getHeight()-1;
-      if(seqCanvas.cursorY<av.startSeq)
-        ap.scrollUp(true);
-      else if(seqCanvas.cursorY+1>av.endSeq)
-        ap.scrollUp(false);
+      else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+        seqCanvas.cursorX = av.alignment.getWidth() - 1;
+
+      if (seqCanvas.cursorY < 0)
+        seqCanvas.cursorY = 0;
+      else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+        seqCanvas.cursorY = av.alignment.getHeight() - 1;
+
 
+      endEditing();
+      if(av.wrapAlignment)
+      {
+        ap.scrollToWrappedVisible(seqCanvas.cursorX);
+      }
+      else
+      {
+        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);
+
       seqCanvas.repaint();
     }
 
@@ -277,7 +372,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       groupEditing = group;
       startseq = seqCanvas.cursorY;
       lastres = seqCanvas.cursorX;
-      editSequence(true, seqCanvas.cursorX+getKeyboardGaps());
+      editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
       editOccurred();
     }
 
@@ -287,26 +382,28 @@ public class SeqPanel extends JPanel implements MouseListener,
                                                    av.alignment, HistoryItem.EDIT));
       groupEditing = group;
       startseq = seqCanvas.cursorY;
-      lastres = seqCanvas.cursorX+getKeyboardGaps();
+      lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
       editSequence(false, seqCanvas.cursorX);
       editOccurred();
     }
 
     void numberPressed(char value)
     {
-      if(keyboardGaps==null)
-        keyboardGaps = new StringBuffer();
+      if(keyboardNo1==null)
+        keyboardNo1 = new StringBuffer();
 
-      keyboardGaps.append(value);
+      if(keyboardNo2!=null)
+        keyboardNo2.append(value);
+      else
+        keyboardNo1.append(value);
     }
 
-    StringBuffer keyboardGaps;
-    int getKeyboardGaps()
+    int getKeyboardNo(StringBuffer kb)
     {
-      if(keyboardGaps==null)
+      if(kb==null)
         return 1;
       else
-        return Integer.parseInt(keyboardGaps.toString());
+        return Integer.parseInt(kb.toString());
     }
 
 
@@ -341,6 +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;
@@ -430,6 +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++)
               {
@@ -451,30 +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("");
@@ -526,6 +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);
@@ -558,40 +722,31 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     }
 
-    void editSequence(boolean insertGap, int startres)
+    synchronized void editSequence(boolean insertGap, int startres)
     {
       int fixedLeft = -1;
       int fixedRight = -1;
       boolean fixedColumns = false;
+      SequenceGroup sg = av.getSelectionGroup();
 
-       if(insertGap && av.hasHiddenColumns)
-        {
-          //Stop editing if the user has dragged beyond hiddenBoundary
-          fixedRight = av.getColumnSelection().getHiddenRegionBoundary(lastres);
-          if( fixedRight < lastres)
-          {
-            if(lastres!=fixedRight)
-            {
-              endEditing();
-              return;
-            }
-          }
-        }
+      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;
           }
         }
 
-
         SequenceI seq = av.alignment.getSequenceAt(startseq);
         StringBuffer message = new StringBuffer();
         if (groupEditing)
-          message.append("Edit group:");
-       else
+           message.append("Edit group:");
+        else
             message.append("Edit sequence: "+seq.getName());
 
        if(insertGap)
@@ -605,13 +760,12 @@ public class SeqPanel extends JPanel implements MouseListener,
 
         //Are we editing within a selection group?
         if (groupEditing
-            || (av.getSelectionGroup() != null &&
-                av.getSelectionGroup().sequences.contains(seq)))
+            || (sg != null && sg.sequences.contains(seq)))
         {
           fixedColumns = true;
 
-          fixedLeft = av.getSelectionGroup().getStartRes();
-          fixedRight = av.getSelectionGroup().getEndRes();
+          fixedLeft = sg.getStartRes();
+          fixedRight = sg.getEndRes();
 
           if (   (startres < fixedLeft && lastres >= fixedLeft)
               || (startres >= fixedLeft && lastres < fixedLeft)
@@ -634,17 +788,31 @@ 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)
         {
-          SequenceGroup sg = av.getSelectionGroup();
-          if(fixedLeft>sg.getEndRes()
-          ||fixedRight<sg.getStartRes())
-       {
-         endEditing();
-         return;
-       }
 
-          if (av.hasHiddenRows)
+          /*if (av.hasHiddenRows)
           {
             //sg might be null as the user may only see 1 sequence
             if (sg == null)
@@ -669,67 +837,67 @@ public class SeqPanel extends JPanel implements MouseListener,
             }
 
             sg = tmp;
-          }
-
-          if (sg == null)
-          {
-            endEditing();
-            return;
-          }
+          }*/
+          // int blankColumn = -1;
 
-         // int blankColumn = -1;
 
           // drag to right
           if (insertGap)
           {
-            // Is it valid??
+              //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())
+              {
+                sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+                fixedRight = sg.getEndRes();
+              }
+
+            // Is it valid with fixed columns??
             // Find the next gap before the end
             // of the visible region boundary
-            if (av.hasHiddenColumns)
+            boolean blank = false;
+            for (fixedRight = fixedRight;
+                 fixedRight > lastres;
+                 fixedRight--)
             {
-             // int lastCol = av.getColumnSelection().
-             //     getHiddenRegionBoundary(res);
-
-            }
-
-              if (fixedRight != startres && fixedRight<av.alignment.getWidth()-1)
+              blank = true;
+              for (int s = 0; s < sg.getSize(); s++)
               {
-                for (fixedRight = fixedRight;
-                     fixedRight > lastres;
-                     fixedRight --)
+                seq = sg.getSequenceAt(s);
+                for (int j = 0; j < startres - lastres; j++)
                 {
-                  boolean blank = true;
-                  for (int s = 0; s < sg.getSize(); s++)
+                  if (!jalview.util.Comparison.isGap(
+                      seq.getCharAt(fixedRight - j)))
                   {
-                    seq = sg.getSequenceAt(s);
-
-                    if (seq.getSequence().length() <= fixedRight)
-                    {
-                      continue;
-                    }
-
-                    if (!jalview.util.Comparison.isGap(
-                        seq.getCharAt(fixedRight)))
-                    {
-                      blank = false;
-                      continue;
-                    }
-                  }
-                  if (blank)
+                    blank = false;
                     break;
+                  }
                 }
               }
+              if (blank)
+                break;
+            }
 
-              if (fixedRight <= startres)
+            if (!blank)
+            {
+              if(sg.getSize() == av.alignment.getHeight())
+              {
+                //We can still insert gaps if the selectionGroup
+                //contains all the sequences
+                sg.setEndRes(sg.getEndRes()+startres-lastres);
+                fixedRight = av.alignment.getWidth()+startres-lastres;
+              }
+              else
               {
                 endEditing();
                 return;
               }
             }
+          }
 
 
           // drag to left
-          else
+          else if(!insertGap)
           {
             /// Are we able to delete?
             // ie are all columns blank?
@@ -793,14 +961,26 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         else /////Editing a single sequence///////////
         {
-
           if (insertGap)
           {
             // dragging to the right
             for (int j = lastres; j < startres; j++)
             {
               if (fixedColumns && fixedRight != -1)
-                insertChar(j, seq, fixedRight);
+              {
+                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
                 insertChar(j, seq);
             }
@@ -847,7 +1027,7 @@ public class SeqPanel extends JPanel implements MouseListener,
       for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
       {
         if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
-    {
+        {
           //Theres a space, so break and insert the gap
           break;
         }
@@ -945,7 +1125,7 @@ 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();
@@ -954,10 +1134,13 @@ 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);
@@ -1007,7 +1190,7 @@ 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)
@@ -1052,12 +1235,13 @@ public class SeqPanel extends JPanel implements MouseListener,
                             (allGroups[i].getEndRes() >= res))
                     {
                         stretchGroup = allGroups[i];
-                        av.setSelectionGroup(stretchGroup);
-
                         break;
                     }
                 }
             }
+
+            av.setSelectionGroup(stretchGroup);
+
         }
 
         if (av.cursorMode)
@@ -1069,49 +1253,65 @@ 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");
-            }
+
+          jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+          pop.show(this, evt.getX(), evt.getY());
         }
-        else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+        else if (stretchGroup == null)
         {
-            jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
-            pop.show(this, evt.getX(), evt.getY());
+          //Only if left mouse button do we want to change group sizes
 
-            // edit the properties of existing group
-        }
+          // 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 ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
-        {
+          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();
     }
 
@@ -1178,6 +1378,10 @@ public class SeqPanel extends JPanel implements MouseListener,
         {
           y = av.alignment.getHeight() -1;
         }
+        if(res> av.alignment.getWidth())
+        {
+          res = av.alignment.getWidth()-1;
+        }
 
         if (stretchGroup.getEndRes() == res)
         {
@@ -1263,6 +1467,27 @@ public class SeqPanel extends JPanel implements MouseListener,
         seqCanvas.repaint();
     }
 
+    void scrollCanvas(MouseEvent evt)
+    {
+      if(evt==null)
+      {
+        if(scrollThread!=null)
+        {
+          scrollThread.running = false;
+          scrollThread = null;
+        }
+        mouseDragging = false;
+      }
+      else
+      {
+        if (scrollThread == null)
+          scrollThread = new ScrollThread();
+
+        mouseDragging = true;
+        scrollThread.setEvent(evt);
+      }
+
+    }
 
 
     // this class allows scrolling off the bottom of the visible alignment