X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=8ee0729708b8636d763540d29b7f5b61061c4d70;hb=5a74e4957b86821f2fd0752d1d9bc46ebb3cfdc6;hp=0213565b98f22ce005d8521630e0a8ada21f9621;hpb=6cbc1c23947d6812cf5efa36998f237f60f4cc74;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 0213565..8ee0729 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -24,8 +24,6 @@ import java.awt.*;
 import java.awt.event.*;
 import java.awt.image.*;
 
-import java.util.*;
-
 import javax.swing.*;
 
 
@@ -59,6 +57,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     //Used For mouse Dragging and resizing graphs
     int graphStretch = -1;
     int graphStretchY = -1;
+    int min; //used by mouseDragged to see if user
+    int max; //used by mouseDragged to see if user
+    boolean mouseDragging = false;
 
     /**
      * Creates a new AnnotationPanel object.
@@ -337,34 +338,28 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
-        if (evt.isShiftDown())
-        {
-                /*int start = Integer.parseInt(activeRes.get(activeRes.size() -
-                            1).toString());
-                int end = res;
+        min = res;
+        max = res;
 
-                if (end < start)
-                {
-                    int temp = end;
-                    end = start;
-                    start = temp;
-                }
-
-                for (int n = start; n <= end; n++)
-                {
-                   addEditableColumn(n);
-                } */
-        }
+        if (av.getColumnSelection().contains(res))
+          av.getColumnSelection().removeElement(res);
         else
         {
-          if (av.getColumnSelection().contains(res))
-            av.getColumnSelection().removeElement(res);
-          else
             av.getColumnSelection().addElement(res);
+            SequenceGroup sg = new SequenceGroup();
 
-          ap.repaint();
+            for (int i = 0; i < av.alignment.getSequences().size(); i++)
+            {
+                sg.addSequence(av.alignment.getSequenceAt(i), false);
+            }
 
+            sg.setStartRes(res);
+            sg.setEndRes(res);
+            av.setSelectionGroup(sg);
         }
+
+        ap.repaint();
+
     }
 
     /**
@@ -376,6 +371,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     {
       graphStretch = -1;
       graphStretchY = -1;
+      mouseDragging = false;
     }
 
     /**
@@ -385,6 +381,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */
     public void mouseEntered(MouseEvent evt)
     {
+      if(mouseDragging)
+        ap.seqPanel.scrollCanvas(null);
     }
 
     /**
@@ -394,8 +392,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */
     public void mouseExited(MouseEvent evt)
     {
+      if(mouseDragging)
+        ap.seqPanel.scrollCanvas(evt);
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -412,6 +413,56 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         adjustPanelHeight();
         ap.repaint();
       }
+      else
+      {
+        mouseDragging = true;
+
+        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+        SequenceGroup sg = av.getSelectionGroup();
+
+        if (res < min)
+        {
+            min = res;
+        }
+
+        if (res > max)
+        {
+            max = res;
+        }
+
+        if (sg != null)
+        {
+            if (!av.getColumnSelection().contains(res))
+            {
+                av.getColumnSelection().addElement(res);
+            }
+
+            if (res > sg.getStartRes())
+            {
+                sg.setEndRes(res);
+            }
+            else if (res < sg.getStartRes())
+            {
+                sg.setStartRes(res);
+            }
+
+            for (int i = min; i <= max; i++)
+            {
+                if ((i < sg.getStartRes()) || (i > sg.getEndRes()))
+                {
+                    av.getColumnSelection().removeElement(i);
+                }
+                else
+                {
+                    av.getColumnSelection().addElement(i);
+                }
+            }
+
+            ap.repaint();
+        }
+
+      }
     }
 
     /**
@@ -584,6 +635,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */
     public void drawComponent(Graphics g, int startRes, int endRes)
     {
+
+
       g.setFont(av.getFont());
 
       if (fm == null)
@@ -593,13 +646,14 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         g.setColor(Color.white);
         g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
 
-        if ((av.alignment.getAlignmentAnnotation() == null) ||
+        if ( (av.alignment.getAlignmentAnnotation() == null) ||
                 (av.alignment.getAlignmentAnnotation().length < 1))
         {
             g.setColor(Color.white);
             g.fillRect(0, 0, getWidth(), getHeight());
             g.setColor(Color.black);
-            g.drawString("Alignment has no annotations", 20, 15);
+            if(av.validCharWidth)
+              g.drawString("Alignment has no annotations", 20, 15);
 
             return;
         }
@@ -608,8 +662,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
         int x = 0;
         int y = 0;
-        char[] lastSS = new char[aa.length];
-        int[] lastSSX = new int[aa.length];
+        char lastSS;
+        int lastSSX;
         int iconOffset = av.charHeight / 2;
         boolean validRes = false;
 
@@ -626,6 +680,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 continue;
             }
 
+            lastSS = ' ';
+            lastSSX = 0;
 
 
             if (row.graph>0)
@@ -652,21 +708,17 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             }
 
             int column = startRes;
-            int yPos = startRes;
-            int aaMax = row.annotations.length-1;
 
-            while (yPos < endRes)
+            while (column < endRes)
             {
               if (av.hasHiddenColumns)
               {
-                column = av.getColumnSelection().adjustForHiddenColumns(yPos);
-                if (column > aaMax)
+                column = av.getColumnSelection().adjustForHiddenColumns(column);
+                if (column > row.annotations.length-1)
                 {
                   break;
                 }
               }
-              else
-                column = yPos;
 
                 if ((row.annotations.length <= column) ||
                         (row.annotations[column] == null))
@@ -678,7 +730,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     validRes = true;
                 }
 
-                x = (yPos - startRes) * av.charWidth;
+                x = (column - startRes) * av.charWidth;
 
                 if (activeRow == i)
                 {
@@ -699,7 +751,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     }
                 }
 
-                if (validRes &&
+                if (av.validCharWidth && validRes &&
                         (row.annotations[column].displayCharacter.length() > 0))
                 {
 
@@ -713,9 +765,13 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                         g.drawString(row.annotations[column].displayCharacter, x+charOffset,
                             y + iconOffset + 3);
                     }
-                    else if (((row.annotations[column - 1] == null) ||
-                            (row.annotations[column].displayCharacter != row.annotations[column -
-                            1].displayCharacter)))
+                    else if (
+                        row.annotations[column - 1] == null
+                        ||(!row.annotations[column].displayCharacter.equals(
+                            row.annotations[column - 1].displayCharacter)
+                        ||
+                  (row.annotations[column].displayCharacter.length() <2 &&
+                   row.annotations[column].secondaryStructure==' ')))
                     {
                         g.drawString(row.annotations[column].displayCharacter, x+charOffset,
                             y + iconOffset + 3);
@@ -725,21 +781,37 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 if (row.hasIcons)
                 {
                     if (!validRes ||
-                            (row.annotations[column].secondaryStructure != lastSS[i]))
+                            (row.annotations[column].secondaryStructure != lastSS))
                     {
-                        switch (lastSS[i])
+                        switch (lastSS)
                         {
                         case 'H':
                             g.setColor(HELIX_COLOUR);
-                            g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
-                                x - lastSSX[i], 7, 8, 8);
+                            int sCol = (lastSSX / av.charWidth) + startRes;
+                            int x1 = lastSSX;
+                            int x2 = x;
+
+                           if(row.annotations[sCol-1]==null ||
+                              row.annotations[sCol-1].secondaryStructure!='H')
+                           {
+                             g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;
+                             x1 += av.charWidth/2;
+                           }
+
+                            if(row.annotations[column]==null ||
+                               row.annotations[column].secondaryStructure!='H')
+                            {
+                              g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 8, 270,180);
+                              x2 -= av.charWidth/2;
+                            }
 
+                            g.fillRect(x1, y+4+iconOffset, x2-x1, 8);
                             break;
 
                         case 'E':
                             g.setColor(SHEET_COLOUR);
-                            g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                                x - lastSSX[i] - 4, 7);
+                            g.fillRect(lastSSX, y + 4 + iconOffset,
+                                x - lastSSX - 4, 7);
                             g.fillPolygon(new int[] { x - 4, x - 4, x },
                                 new int[]
                                 {
@@ -752,38 +824,56 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
                         default:
                             g.setColor(Color.gray);
-                            g.fillRect(lastSSX[i], y + 6 + iconOffset,
-                                x - lastSSX[i], 2);
+                            g.fillRect(lastSSX, y + 6 + iconOffset,
+                                x - lastSSX, 2);
 
                             break;
                         }
 
                         if (validRes)
                         {
-                            lastSS[i] = row.annotations[column].secondaryStructure;
+                            lastSS = row.annotations[column].secondaryStructure;
                         }
                         else
                         {
-                            lastSS[i] = ' ';
+                            lastSS = ' ';
                         }
 
-                        lastSSX[i] = x;
+                        lastSSX = x;
                     }
                 }
 
-                yPos++;
+                column++;
             }
 
             x += av.charWidth;
 
             if (row.hasIcons)
             {
-                switch (lastSS[i])
+                switch (lastSS)
                 {
                 case 'H':
-                    g.setColor(HELIX_COLOUR);
-                    g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
-                        x - lastSSX[i], 7, 8, 8);
+                  g.setColor(HELIX_COLOUR);
+
+                  int sCol = (lastSSX / av.charWidth) + startRes;
+                  int x1 = lastSSX;
+                  int x2 = x;
+
+                 if(row.annotations[sCol-1]==null ||
+                    row.annotations[sCol-1].secondaryStructure!='H')
+                 {
+                   g.fillArc(lastSSX, y+4+iconOffset, av.charWidth, 8, 90,180) ;
+                   x1 += av.charWidth/2;
+                 }
+
+                  if(row.annotations[column]==null ||
+                     row.annotations[column].secondaryStructure!='H')
+                  {
+                    g.fillArc(x-av.charWidth, y+4+iconOffset, av.charWidth, 8, 270,180);
+                    x2 -= av.charWidth/2;
+                  }
+
+                  g.fillRect(x1, y+4+iconOffset, x2-x1, 8);
 
                     break;
 
@@ -793,8 +883,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     if (row.annotations[endRes] !=null
                         && row.annotations[endRes].secondaryStructure != 'E')
                     {
-                      g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                                 x - lastSSX[i] - 4, 7);
+                      g.fillRect(lastSSX, y + 4 + iconOffset,
+                                 x - lastSSX - 4, 7);
                       g.fillPolygon(new int[]
                                     {x - 4, x - 4, x},
                                     new int[]
@@ -804,17 +894,16 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                       }, 3);
                     }
                     else
-                      g.fillRect(lastSSX[i], y + 4 + iconOffset,
-                                 x - lastSSX[i], 7);
+                      g.fillRect(lastSSX, y + 4 + iconOffset,
+                                 x - lastSSX, 7);
 
                     break;
 
-                case 'C':
-                    break;
 
                 default:
                     g.setColor(Color.gray);
-                    g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
+                    if(!av.wrapAlignment || endRes==av.endRes)
+                      g.fillRect(lastSSX, y + 6 + iconOffset, x - lastSSX, 2);
 
                     break;
                 }
@@ -883,6 +972,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       if(sRes>aa.annotations.length)
         return;
 
+      eRes = Math.min(eRes, aa.annotations.length);
+
       int x = 0;
 
       //Adjustment for fastpaint to left
@@ -905,45 +996,26 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       g.setColor(Color.gray);
       g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
 
-
-      if(aa.threshold!=null)
-      {
-          g.setColor(aa.threshold.colour);
-          Graphics2D g2 = (Graphics2D)g;
-          g2.setStroke(new BasicStroke(1,
-                                        BasicStroke.CAP_SQUARE,
-                                        BasicStroke.JOIN_ROUND, 3f,
-                                        new float[] { 5f, 3f }, 0f));
-
-          y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
-          g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
-          g2.setStroke(new BasicStroke());
-      }
-
       eRes = Math.min(eRes, aa.annotations.length);
 
       int column = sRes;
-      int yPos = sRes;
       int aaMax = aa.annotations.length-1;
 
-      while( yPos < eRes )
+      while( column < eRes )
       {
         if(av.hasHiddenColumns)
         {
-          column = av.getColumnSelection().adjustForHiddenColumns(yPos);
+          column = av.getColumnSelection().adjustForHiddenColumns(column);
           if(column > aaMax)
           {
             break;
           }
         }
-        else
-          column = yPos;
-
-        yPos ++;
 
         if(aa.annotations[column]==null || aa.annotations[column-1]==null)
         {
           x+=av.charWidth;
+          column ++;
           continue;
         }
 
@@ -952,7 +1024,23 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);
           g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);
           x += av.charWidth;
+
+          column++;
+
        }
+       if(aa.threshold!=null)
+       {
+           g.setColor(aa.threshold.colour);
+           Graphics2D g2 = (Graphics2D)g;
+           g2.setStroke(new BasicStroke(1,
+                                         BasicStroke.CAP_SQUARE,
+                                         BasicStroke.JOIN_ROUND, 3f,
+                                         new float[] { 5f, 3f }, 0f));
+
+           y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight);
+           g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+           g2.setStroke(new BasicStroke());
+      }
     }
 
     public void drawBarGraph(Graphics g, AlignmentAnnotation aa,
@@ -963,24 +1051,12 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       if(sRes>aa.annotations.length)
         return;
 
+      eRes = Math.min(eRes, aa.annotations.length);
+
       int x=0, y1, y2;
 
       float range = max - min;
 
-      if(aa.threshold!=null)
-      {
-          g.setColor(aa.threshold.colour);
-          Graphics2D g2 = (Graphics2D)g;
-          g2.setStroke(new BasicStroke(1,
-                                        BasicStroke.CAP_SQUARE,
-                                        BasicStroke.JOIN_ROUND, 3f,
-                                        new float[] { 5f, 3f }, 0f));
-
-          y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
-          g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);
-          g2.setStroke(new BasicStroke());
-      }
-
       y1 = y2 = y;
 
       if(min<0)
@@ -988,35 +1064,30 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 
       g.setColor(Color.gray);
 
-      g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2);
+      g.drawLine(x,y2,(eRes-sRes)*av.charWidth,y2);
 
 
       int column = sRes;
-      int yPos = sRes;
       int aaMax = aa.annotations.length-1;
 
-      while( yPos < eRes )
+      while( column < eRes )
       {
         if(av.hasHiddenColumns)
         {
-          column = av.getColumnSelection().adjustForHiddenColumns(yPos);
+          column = av.getColumnSelection().adjustForHiddenColumns(column);
           if(column > aaMax)
           {
             break;
           }
         }
-        else
-          column = yPos;
-
-        yPos ++;
 
         if (aa.annotations[column] == null)
         {
           x += av.charWidth;
+          column ++;
           continue;
         }
 
-
           g.setColor(aa.annotations[column].colour);
           y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);
 
@@ -1026,8 +1097,22 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             g.fillRect(x, y1, av.charWidth, y2-y1 );
 
           x += av.charWidth;
+          column ++;
+
       }
+      if(aa.threshold!=null)
+      {
+          g.setColor(aa.threshold.colour);
+          Graphics2D g2 = (Graphics2D)g;
+          g2.setStroke(new BasicStroke(1,
+                                        BasicStroke.CAP_SQUARE,
+                                        BasicStroke.JOIN_ROUND, 3f,
+                                        new float[] { 5f, 3f }, 0f));
 
+          y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight);
+          g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);
+          g2.setStroke(new BasicStroke());
+      }
     }
 
     // used by overview window