GraphGroups added

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 560c983..7418e48 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -182,15 +182,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 \r
 \r
         ap.annotationPanel.adjustPanelHeight();\r
-\r
-        Dimension d = ap.annotationScroller.getPreferredSize();\r
-        ap.annotationScroller.setPreferredSize(new Dimension(d.width,\r
-                d.height + dif));\r
-        d = ap.annotationSpaceFillerHolder.getPreferredSize();\r
-        ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(d.width,\r
-                d.height + dif));\r
-\r
-        ap.addNotify();\r
+        ap.annotationScroller.validate();\r
+        ap.repaint();\r
     }\r
 \r
     /**\r
@@ -363,6 +356,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
          width = ap.calculateIdWidth().width + 4;\r
 \r
        Graphics2D g2 = (Graphics2D) g;\r
+       if(av.antiAlias)\r
         g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
             RenderingHints.VALUE_ANTIALIAS_ON);\r
 \r
@@ -390,8 +384,11 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         g.setColor(Color.black);\r
 \r
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-        int y = g.getFont().getSize();\r
+        int fontHeight = g.getFont().getSize();\r
+        int y = fontHeight;\r
         int x = 0;\r
+        int graphExtras = 0;\r
+\r
 \r
 \r
         if (aa != null)\r
@@ -407,13 +404,71 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 \r
                 if (aa[i].graph>0)\r
                 {\r
+                    graphExtras = y;\r
+\r
                     y += (aa[i].height / 3);\r
+\r
+                    if(aa[i].graphGroup<0)\r
+                        graphExtras = y + fontHeight;\r
                 }\r
 \r
-                g.drawString(aa[i].label, x, y);\r
+                if(aa[i].graphGroup>-1)\r
+                {\r
+                  int groupSize = 0;\r
+                  for (int gg = 0; gg < aa.length; gg++)\r
+                  {\r
+                    if (aa[gg].graphGroup == aa[i].graphGroup)\r
+                      groupSize++;\r
+                  }\r
+\r
+                  if(groupSize * (fontHeight+8) < aa[i].height)\r
+                    graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;\r
+\r
+                 for(int gg=0; gg<aa.length; gg++)\r
+                 {\r
+                   if(aa[gg].graphGroup==aa[i].graphGroup)\r
+                   {\r
+                     x = width - fm.stringWidth(aa[gg].label) - 3;\r
+                     g.drawString(aa[gg].label, x, graphExtras );\r
+                     if(aa[gg].annotations[0]!=null)\r
+                       g.setColor(aa[gg].annotations[0].colour);\r
+\r
+                     g.drawLine( x, graphExtras+3,\r
+                                 x+fm.stringWidth(aa[gg].label),\r
+                                 graphExtras+3);\r
+\r
+                     g.setColor(Color.black);\r
+                     graphExtras += fontHeight+8;\r
+                   }\r
+                 }\r
+                }\r
+                else\r
+                  g.drawString(aa[i].label, x, y);\r
 \r
                 if (aa[i].graph>0)\r
                 {\r
+                  if (aa[i].graphLines != null)\r
+                  {\r
+                    for (int gl = 0; gl < aa[i].graphLines.size(); gl++)\r
+                    {\r
+                       x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;\r
+                      g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);\r
+                      g.setColor(aa[i].getGraphLine(gl).colour);\r
+                      Graphics2D g2 = (Graphics2D) g;\r
+                      g2.setStroke(new BasicStroke(1,\r
+                          BasicStroke.CAP_SQUARE,\r
+                          BasicStroke.JOIN_ROUND, 3f,\r
+                          new float[]\r
+                          {5f, 3f}, 0f));\r
+\r
+                      graphExtras += 3;\r
+\r
+                      g.drawLine(x, graphExtras,\r
+                                 x+fm.stringWidth(aa[i].label),\r
+                                 graphExtras);\r
+                      g2.setStroke(new BasicStroke());\r
+                    }\r
+                  }\r
                     y += ((2 * aa[i].height) / 3);\r
                 }\r
                 else\r
@@ -427,7 +482,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         {\r
             if (image != null)\r
             {\r
-                g.drawImage(image, 2, 0, this);\r
+                g.drawImage(image, 2, 0 - scrollOffset, this);\r
             }\r
         }\r
 \r

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 8f72f71..3a4a197 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -38,16 +38,15 @@ import javax.swing.*;
 public class AnnotationPanel extends JPanel implements MouseListener,\r
     MouseMotionListener, ActionListener, AdjustmentListener\r
 {\r
-    static String HELIX = "Helix";\r
-    static String SHEET = "Sheet";\r
-    static String LABEL = "Label";\r
-    static String REMOVE = "Remove Annotation";\r
-    static String COLOUR = "Colour";\r
-    static Color HELIX_COLOUR = Color.red.darker();\r
-    static Color SHEET_COLOUR = Color.green.darker().darker();\r
+    final String HELIX = "Helix";\r
+    final String SHEET = "Sheet";\r
+    final String LABEL = "Label";\r
+    final String REMOVE = "Remove Annotation";\r
+    final String COLOUR = "Colour";\r
+    final Color HELIX_COLOUR = Color.red.darker();\r
+    final Color SHEET_COLOUR = Color.green.darker().darker();\r
 \r
     /** DOCUMENT ME!! */\r
-    public static int GRAPH_HEIGHT = 40;\r
     AlignViewport av;\r
     AlignmentPanel ap;\r
     int activeRow = -1;\r
@@ -58,6 +57,10 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     int imgWidth = 0;\r
     boolean fastPaint = false;\r
 \r
+    //Used For mouse Dragging and resizing graphs\r
+    int graphStretch = -1;\r
+    int graphStretchY = -1;\r
+\r
     /**\r
      * Creates a new AnnotationPanel object.\r
      *\r
@@ -125,7 +128,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
                 if (aa[i].graph>0)\r
                 {\r
-                    aa[i].height += GRAPH_HEIGHT;\r
+                    aa[i].height += aa[i].graphHeight;\r
                 }\r
 \r
                 if (aa[i].height == 0)\r
@@ -342,6 +345,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         activeRow = -1;\r
 \r
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
+        if(aa==null)\r
+          return;\r
 \r
         for (int i = 0; i < aa.length; i++)\r
         {\r
@@ -356,6 +361,23 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 {\r
                     activeRow = i;\r
                 }\r
+                else if(aa[i].graph>0)\r
+                {\r
+                  if(SwingUtilities.isRightMouseButton(evt)\r
+                      && aa[i].graphLines!=null\r
+                       && aa[i].graphLines.size()>0)\r
+                  {\r
+                    SliderPanel sp = new SliderPanel(aa[i], ap);\r
+                    return;\r
+                  }\r
+                  else\r
+                  {\r
+                    //Stretch Graph\r
+                    graphStretch = i;\r
+                    graphStretchY = evt.getY();\r
+                    activeRes = null;\r
+                  }\r
+                }\r
                 else\r
                 {\r
                     activeRes = null;\r
@@ -434,8 +456,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             activeRes = new Vector();\r
             activeRes.addElement(String.valueOf(res));\r
         }\r
-\r
-        repaint();\r
     }\r
 \r
     /**\r
@@ -445,6 +465,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */\r
     public void mouseReleased(MouseEvent evt)\r
     {\r
+      graphStretch = -1;\r
+      graphStretchY = -1;\r
     }\r
 \r
     /**\r
@@ -472,6 +494,15 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */\r
     public void mouseDragged(MouseEvent evt)\r
     {\r
+      if(graphStretch>-1)\r
+      {\r
+        av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY();\r
+        if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <10)\r
+          av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 10;\r
+        graphStretchY = evt.getY();\r
+        adjustPanelHeight();\r
+        ap.repaint();\r
+      }\r
     }\r
 \r
     /**\r
@@ -511,7 +542,21 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         if ((row > -1) && (res < aa[row].annotations.length) &&\r
                 (aa[row].annotations[res] != null))\r
         {\r
-            this.setToolTipText(aa[row].annotations[res].description);\r
+\r
+\r
+            if(aa[row].graphGroup>-1)\r
+            {\r
+              StringBuffer tip = new StringBuffer("<html>");\r
+              for (int gg = 0; gg < aa.length; gg++)\r
+              {\r
+                if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null)\r
+                  tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"<br>" );\r
+              }\r
+              tip.setLength(tip.length()-4);\r
+              this.setToolTipText(tip.toString()+"</html>");\r
+            }\r
+            else\r
+              this.setToolTipText(aa[row].annotations[res].description);\r
 \r
             StringBuffer text = new StringBuffer("Sequence position " +\r
                     (res + 1) + "  " + aa[row].annotations[res].description);\r
@@ -538,20 +583,26 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       g.setColor(Color.white);\r
       g.fillRect(0, 0, getWidth(), getHeight());\r
 \r
-      if (fastPaint && image!=null)\r
-      {\r
-        g.drawImage(image, 0, 0, this);\r
-        fastPaint = false;\r
-        return;\r
+      if(image!=null)\r
+      {if (fastPaint\r
+            || (getVisibleRect().width != g.getClipBounds().width)\r
+            || (getVisibleRect().height != g.getClipBounds().height))\r
+        {\r
+          g.drawImage(image, 0, 0, this);\r
+          fastPaint = false;\r
+          return;\r
+        }\r
       }\r
-\r
       imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;\r
 \r
-      if (image == null || imgWidth != image.getWidth())\r
+      if (image == null || imgWidth != image.getWidth()\r
+          || image.getHeight(this) != getHeight())\r
       {\r
         image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),\r
                                   BufferedImage.TYPE_INT_RGB);\r
         gg = (Graphics2D) image.getGraphics();\r
+\r
+        if(av.antiAlias)\r
         gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
                             RenderingHints.VALUE_ANTIALIAS_ON);\r
 \r
@@ -559,6 +610,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         fm = gg.getFontMetrics();\r
       }\r
 \r
+\r
       drawComponent(gg, av.startRes, av.endRes + 1);\r
       g.drawImage(image, 0, 0, this);\r
     }\r
@@ -575,7 +627,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 (av.alignment.getAlignmentAnnotation().length < 1))\r
         {\r
             repaint();\r
-\r
             return;\r
         }\r
 \r
@@ -646,6 +697,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         int iconOffset = av.charHeight / 2;\r
         boolean validRes = false;\r
 \r
+        boolean [] graphGroupDrawn = new boolean[aa.length];\r
+\r
+\r
         //\u03B2 \u03B1\r
         for (int i = 0; i < aa.length; i++)\r
         {\r
@@ -659,6 +713,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
             if (row.graph>0)\r
             {\r
+                if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] )\r
+                  continue;\r
+\r
                 // this is so that we draw the characters below the graph\r
                 y += row.height;\r
 \r
@@ -760,8 +817,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
                             break;\r
 \r
-                        case 'C':\r
-                            break;\r
 \r
                         default:\r
                             g.setColor(Color.gray);\r
@@ -783,21 +838,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                         lastSSX[i] = x;\r
                     }\r
                 }\r
-\r
-                if (validRes && row.graph>0)\r
-                {\r
-                    ///g.setColor(new Color(0, 0, 180));\r
-\r
-                    if(row.graph== AlignmentAnnotation.LINE_GRAPH )\r
-                        drawLineGraph(g, row, j, j+1, x, y);\r
-                    else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
-                       drawBarGraph(g, row, j, j+1, x, y);\r
-\r
-                    //int height = (int) ((row.annotations[j].value / row.graphMax) * GRAPH_HEIGHT);\r
-\r
-                   // g.setColor(row.annotations[j].colour);\r
-                   // g.fillRect(x, y - height, av.charWidth, height);\r
-                }\r
             }\r
 \r
             x += av.charWidth;\r
@@ -815,14 +855,22 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
                 case 'E':\r
                     g.setColor(SHEET_COLOUR);\r
-                    g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
-                        x - lastSSX[i] - 4, 7);\r
-                    g.fillPolygon(new int[] { x - 4, x - 4, x },\r
-                        new int[]\r
-                        {\r
-                            y + iconOffset, y + 14 + iconOffset,\r
-                            y + 7 + iconOffset\r
-                        }, 3);\r
+\r
+                    if (row.annotations[endRes].secondaryStructure != 'E')\r
+                    {\r
+                      g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
+                                 x - lastSSX[i] - 4, 7);\r
+                      g.fillPolygon(new int[]\r
+                                    {x - 4, x - 4, x},\r
+                                    new int[]\r
+                                    {\r
+                                    y + iconOffset, y + 14 + iconOffset,\r
+                                    y + 7 + iconOffset\r
+                      }, 3);\r
+                    }\r
+                    else\r
+                      g.fillRect(lastSSX[i], y + 4 + iconOffset,\r
+                                 x - lastSSX[i], 7);\r
 \r
                     break;\r
 \r
@@ -837,6 +885,48 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 }\r
             }\r
 \r
+            if (row.graph>0)\r
+            {\r
+                if(row.graph == AlignmentAnnotation.LINE_GRAPH )\r
+                {\r
+                  if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup])\r
+                   {\r
+                     float groupmax=-999999, groupmin=9999999;\r
+                     for(int gg=0; gg<aa.length; gg++)\r
+                     {\r
+                       if(aa[gg].graphGroup!=row.graphGroup)\r
+                         continue;\r
+\r
+                       if(aa[gg]!=row)\r
+                         aa[gg].visible = false;\r
+\r
+                       if(aa[gg].graphMax>groupmax)\r
+                         groupmax = aa[gg].graphMax;\r
+                       if(aa[gg].graphMin<groupmin)\r
+                         groupmin = aa[gg].graphMin;\r
+                     }\r
+\r
+                     for (int gg = 0; gg < aa.length; gg++)\r
+                     {\r
+                       if (aa[gg].graphGroup == row.graphGroup)\r
+                       {\r
+                         drawLineGraph(g, aa[gg], startRes, endRes, y,\r
+                                       groupmin, groupmax,\r
+                                       row.graphHeight);\r
+                       }\r
+                     }\r
+\r
+                     graphGroupDrawn[ row.graphGroup ] = true;\r
+                   }\r
+                   else\r
+                     drawLineGraph(g, row, startRes, endRes,\r
+                                   y, row.graphMin, row.graphMax, row.graphHeight  );\r
+                }\r
+                else if(row.graph == AlignmentAnnotation.BAR_GRAPH )\r
+                   drawBarGraph(g, row, startRes, endRes,\r
+                                row.graphMin, row.graphMax, y);\r
+            }\r
+\r
             if (row.graph>0 && row.hasText)\r
             {\r
                 y += av.charHeight;\r
@@ -849,39 +939,130 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }\r
     }\r
 \r
-    public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, int x, int y)\r
+    public void drawLineGraph(Graphics g, AlignmentAnnotation aa,\r
+                              int sRes, int eRes,\r
+                              int y,\r
+                              float min, float max,\r
+                              int graphHeight)\r
     {\r
-      g.setColor(new Color(0, 0, 0));\r
+      if(sRes>aa.annotations.length)\r
+        return;\r
+\r
+      int x = 0;\r
+\r
+      //Adjustment for fastpaint to left\r
+      if(eRes<av.endRes)\r
+        eRes++;\r
+\r
       if(sRes==0)\r
+      {\r
         sRes++;\r
+        x+=av.charWidth;\r
+      }\r
 \r
       int y1=y, y2=y;\r
-      for (int j = sRes; j < eRes; j++)\r
-      {\r
-          if(aa.annotations[j-1]!=null)\r
-            y1 = y - (int) ((aa.annotations[j-1].value / aa.graphMax) * GRAPH_HEIGHT);\r
+      float range = max - min;\r
 \r
-          if(aa.annotations[j]!=null)\r
-          y2 = y - (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
+      ////Draw origin\r
+      if(min<0)\r
+        y2 = (int)(y - (0-min / range)*graphHeight);\r
 \r
-          g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
+      g.setColor(Color.gray);\r
+      g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
 \r
-          x += av.charWidth;\r
+\r
+      if(aa.graphLines!=null)\r
+      {\r
+        for(int l=0; l<aa.graphLines.size(); l++)\r
+        {\r
+          g.setColor(aa.getGraphLine(l).colour);\r
+          Graphics2D g2 = (Graphics2D)g;\r
+          g2.setStroke(new BasicStroke(1,\r
+                                        BasicStroke.CAP_SQUARE,\r
+                                        BasicStroke.JOIN_ROUND, 3f,\r
+                                        new float[] { 5f, 3f }, 0f));\r
+\r
+          y2 = (int)(y - ((aa.getGraphLine(l).value-min) / range)*graphHeight);\r
+          g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
+          g2.setStroke(new BasicStroke());\r
         }\r
+      }\r
+\r
+      eRes = Math.min(eRes, aa.annotations.length);\r
+      for (int j = sRes; j < eRes; j++)\r
+      {\r
+        if(aa.annotations[j]==null || aa.annotations[j-1]==null)\r
+        {\r
+          x+=av.charWidth;\r
+          continue;\r
+        }\r
+          g.setColor(aa.annotations[j].colour);\r
+          y1 = y - (int) (((aa.annotations[j-1].value-min) / range) * graphHeight);\r
+          y2 = y - (int) (((aa.annotations[j].value-min) / range) * graphHeight);\r
+          g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
+          x += av.charWidth;\r
+       }\r
     }\r
 \r
-    public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, int x, int y)\r
+    public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
+                             int sRes, int eRes,\r
+                             float min, float max,\r
+                             int y)\r
     {\r
-      g.setColor(new Color(0, 0, 180));\r
-      int j, height=0;\r
-      for (j = sRes; j < eRes; j++)\r
+      if(sRes>aa.annotations.length)\r
+        return;\r
+\r
+      int x=0, y1, y2;\r
+\r
+      float range = max - min;\r
+\r
+      if(aa.graphLines!=null)\r
       {\r
-          g.setColor(aa.annotations[j].colour);\r
-          height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);\r
+        for(int l=0; l<aa.graphLines.size(); l++)\r
+        {\r
+          g.setColor(aa.getGraphLine(l).colour);\r
+          Graphics2D g2 = (Graphics2D)g;\r
+          g2.setStroke(new BasicStroke(1,\r
+                                        BasicStroke.CAP_SQUARE,\r
+                                        BasicStroke.JOIN_ROUND, 3f,\r
+                                        new float[] { 5f, 3f }, 0f));\r
+\r
+          y2 = (int)(y - ((aa.getGraphLine(l).value-min) / range)*aa.graphHeight);\r
+          g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
+          g2.setStroke(new BasicStroke());\r
+        }\r
+      }\r
 \r
-          g.fillRect(x, y - height, av.charWidth, height);\r
+      y1 = y2 = y;\r
+\r
+      if(min<0)\r
+        y2 = (int)(y - (0-min / (range))*aa.graphHeight);\r
+\r
+      g.setColor(Color.gray);\r
+      g.drawLine(x,y2,eRes*av.charWidth,y2);\r
+\r
+      eRes = Math.min(eRes, aa.annotations.length-1);\r
+\r
+\r
+      for (int j = sRes; j < eRes; j++)\r
+      {\r
+        if (aa.annotations[j] == null)\r
+        {\r
           x += av.charWidth;\r
+          continue;\r
         }\r
+\r
+          g.setColor(aa.annotations[j].colour);\r
+          y1 = y - (int) (((aa.annotations[j].value-min) / (range)) * aa.graphHeight);\r
+\r
+          if(y1-y2>0)\r
+            g.fillRect(x, y2, av.charWidth, y1-y2 );\r
+          else\r
+            g.fillRect(x, y1, av.charWidth, y2-y1 );\r
+\r
+          x += av.charWidth;\r
+      }\r
+\r
     }\r
 \r
     // used by overview window\r
@@ -895,7 +1076,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
       for (int j = sRes; j < eRes; j++)\r
       {\r
-          g.setColor(new Color(0, 0, 180));\r
+          g.setColor(aa.annotations[j].colour);\r
 \r
           height = (int) ((aa.annotations[j].value / aa.graphMax) * y);\r
           if(height>y)\r