Allow for hidden columns

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 69ae398..0213565 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -50,7 +50,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     AlignViewport av;\r
     AlignmentPanel ap;\r
     int activeRow = -1;\r
-    Vector activeRes;\r
     BufferedImage image;\r
     Graphics2D gg;\r
     FontMetrics fm;\r
@@ -149,74 +148,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         return height;\r
     }\r
 \r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param col DOCUMENT ME!\r
-     */\r
-    public void removeEditableColumn(int col)\r
-    {\r
-        if (activeRow == -1)\r
-        {\r
-            AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-            if(aa==null)\r
-              return;\r
-\r
-            for (int j = 0; j < aa.length; j++)\r
-            {\r
-                if (aa[j].editable)\r
-                {\r
-                    activeRow = j;\r
-\r
-                    break;\r
-                }\r
-            }\r
-        }\r
-\r
-        if ((activeRes != null) && activeRes.contains(String.valueOf(col)))\r
-        {\r
-            activeRes.removeElement(String.valueOf(col));\r
-        }\r
-\r
-        repaint();\r
-    }\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @param col DOCUMENT ME!\r
-     */\r
-    public void addEditableColumn(int col)\r
-    {\r
-        if (activeRow == -1)\r
-        {\r
-            AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
-            if(aa==null)\r
-              return;\r
-\r
-            for (int j = 0; j < aa.length; j++)\r
-            {\r
-                if (aa[j].editable)\r
-                {\r
-                    activeRow = j;\r
-\r
-                    break;\r
-                }\r
-            }\r
-        }\r
-\r
-        if (activeRes == null)\r
-        {\r
-            activeRes = new Vector();\r
-        }\r
-\r
-        if (!activeRes.contains(String.valueOf(col)))\r
-        {\r
-            activeRes.addElement(String.valueOf(col));\r
-        }\r
 \r
-        repaint();\r
-    }\r
 \r
     /**\r
      * DOCUMENT ME!\r
@@ -230,10 +162,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
         if (evt.getActionCommand().equals(REMOVE))\r
         {\r
-            for (int i = 0; i < activeRes.size(); i++)\r
+            for (int i = 0; i < av.getColumnSelection().size(); i++)\r
             {\r
-                anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
-                anot[Integer.parseInt(activeRes.get(i).toString())] = null;\r
+                anot[av.getColumnSelection().columnAt(i)] = null;\r
             }\r
         }\r
         else if (evt.getActionCommand().equals(LABEL))\r
@@ -251,9 +182,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 aa[activeRow].hasText = true;\r
             }\r
 \r
-            for (int i = 0; i < activeRes.size(); i++)\r
+            for (int i = 0; i < av.getColumnSelection().size(); i++)\r
             {\r
-                int index = Integer.parseInt(activeRes.get(i).toString());\r
+                int index = av.getColumnSelection().columnAt(i);\r
 \r
                 if (anot[index] == null)\r
                 {\r
@@ -268,9 +199,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
             Color col = JColorChooser.showDialog(this,\r
                     "Choose foreground colour", Color.black);\r
 \r
-            for (int i = 0; i < activeRes.size(); i++)\r
+            for (int i = 0; i < av.getColumnSelection().size(); i++)\r
             {\r
-                int index = Integer.parseInt(activeRes.get(i).toString());\r
+                int index = av.getColumnSelection().columnAt(i);\r
 \r
                 if (anot[index] == null)\r
                 {\r
@@ -313,9 +244,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 aa[activeRow].hasText = true;\r
             }\r
 \r
-            for (int i = 0; i < activeRes.size(); i++)\r
+            for (int i = 0; i < av.getColumnSelection().size(); i++)\r
             {\r
-                int index = Integer.parseInt(activeRes.get(i).toString());\r
+                int index = av.getColumnSelection().columnAt(i);\r
 \r
                 if (anot[index] == null)\r
                 {\r
@@ -328,7 +259,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         }\r
 \r
         adjustPanelHeight();\r
-        activeRes = null;\r
         repaint();\r
 \r
         return;\r
@@ -366,11 +296,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     //Stretch Graph\r
                     graphStretch = i;\r
                     graphStretchY = evt.getY();\r
-                    activeRes = null;\r
-                }\r
-                else\r
-                {\r
-                    activeRes = null;\r
                 }\r
 \r
                 break;\r
@@ -379,7 +304,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
         if (SwingUtilities.isRightMouseButton(evt))\r
         {\r
-            if (activeRes == null)\r
+            if (av.getColumnSelection() == null)\r
             {\r
                 return;\r
             }\r
@@ -412,19 +337,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 \r
-        if (evt.isControlDown() || evt.isAltDown())\r
+        if (evt.isShiftDown())\r
         {\r
-            addEditableColumn(res);\r
-        }\r
-        else if (evt.isShiftDown())\r
-        {\r
-            if (activeRes == null)\r
-            {\r
-                activeRes = new Vector();\r
-            }\r
-            else\r
-            {\r
-                int start = Integer.parseInt(activeRes.get(activeRes.size() -\r
+                /*int start = Integer.parseInt(activeRes.get(activeRes.size() -\r
                             1).toString());\r
                 int end = res;\r
 \r
@@ -437,14 +352,18 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
                 for (int n = start; n <= end; n++)\r
                 {\r
-                    addEditableColumn(n);\r
-                }\r
-            }\r
+                   addEditableColumn(n);\r
+                } */\r
         }\r
         else\r
         {\r
-            activeRes = new Vector();\r
-            activeRes.addElement(String.valueOf(res));\r
+          if (av.getColumnSelection().contains(res))\r
+            av.getColumnSelection().removeElement(res);\r
+          else\r
+            av.getColumnSelection().addElement(res);\r
+\r
+          ap.repaint();\r
+\r
         }\r
     }\r
 \r
@@ -529,6 +448,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 \r
+        if(av.hasHiddenColumns)\r
+          res = av.getColumnSelection().adjustForHiddenColumns(res);\r
+\r
         if (row > -1 && res<aa[row].annotations.length)\r
         {\r
             if(aa[row].graphGroup>-1)\r
@@ -684,7 +606,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
         AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();\r
 \r
-        int j;\r
         int x = 0;\r
         int y = 0;\r
         char[] lastSS = new char[aa.length];\r
@@ -730,10 +651,25 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 iconOffset = 0;\r
             }\r
 \r
-            for (j = startRes; j < endRes; j++)\r
+            int column = startRes;\r
+            int yPos = startRes;\r
+            int aaMax = row.annotations.length-1;\r
+\r
+            while (yPos < endRes)\r
             {\r
-                if ((row.annotations.length <= j) ||\r
-                        (row.annotations[j] == null))\r
+              if (av.hasHiddenColumns)\r
+              {\r
+                column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+                if (column > aaMax)\r
+                {\r
+                  break;\r
+                }\r
+              }\r
+              else\r
+                column = yPos;\r
+\r
+                if ((row.annotations.length <= column) ||\r
+                        (row.annotations[column] == null))\r
                 {\r
                     validRes = false;\r
                 }\r
@@ -742,21 +678,21 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                     validRes = true;\r
                 }\r
 \r
-                x = (j - startRes) * av.charWidth;\r
+                x = (yPos - startRes) * av.charWidth;\r
 \r
                 if (activeRow == i)\r
                 {\r
                     g.setColor(Color.red);\r
 \r
-                    if (activeRes != null)\r
+                    if (av.getColumnSelection() != null)\r
                     {\r
-                        for (int n = 0; n < activeRes.size(); n++)\r
+                        for (int n = 0; n < av.getColumnSelection().size(); n++)\r
                         {\r
-                            int v = Integer.parseInt(activeRes.get(n).toString());\r
+                            int v = av.getColumnSelection().columnAt(n);\r
 \r
-                            if (v == j)\r
+                            if (v == column)\r
                             {\r
-                                g.fillRect((j - startRes) * av.charWidth, y,\r
+                                g.fillRect((column - startRes) * av.charWidth, y,\r
                                     av.charWidth, row.height);\r
                             }\r
                         }\r
@@ -764,24 +700,24 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 }\r
 \r
                 if (validRes &&\r
-                        (row.annotations[j].displayCharacter.length() > 0))\r
+                        (row.annotations[column].displayCharacter.length() > 0))\r
                 {\r
 \r
                     int charOffset = (av.charWidth -\r
-                        fm.charWidth(row.annotations[j].displayCharacter.charAt(\r
+                        fm.charWidth(row.annotations[column].displayCharacter.charAt(\r
                                 0))) / 2;\r
-                    g.setColor(row.annotations[j].colour);\r
+                    g.setColor(row.annotations[column].colour);\r
 \r
-                    if (j == 0 || row.graph>0)\r
+                    if (column == 0 || row.graph>0)\r
                     {\r
-                        g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
+                        g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
                             y + iconOffset + 3);\r
                     }\r
-                    else if (((row.annotations[j - 1] == null) ||\r
-                            (row.annotations[j].displayCharacter != row.annotations[j -\r
+                    else if (((row.annotations[column - 1] == null) ||\r
+                            (row.annotations[column].displayCharacter != row.annotations[column -\r
                             1].displayCharacter)))\r
                     {\r
-                        g.drawString(row.annotations[j].displayCharacter, x+charOffset,\r
+                        g.drawString(row.annotations[column].displayCharacter, x+charOffset,\r
                             y + iconOffset + 3);\r
                     }\r
                 }\r
@@ -789,7 +725,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                 if (row.hasIcons)\r
                 {\r
                     if (!validRes ||\r
-                            (row.annotations[j].secondaryStructure != lastSS[i]))\r
+                            (row.annotations[column].secondaryStructure != lastSS[i]))\r
                     {\r
                         switch (lastSS[i])\r
                         {\r
@@ -824,7 +760,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
                         if (validRes)\r
                         {\r
-                            lastSS[i] = row.annotations[j].secondaryStructure;\r
+                            lastSS[i] = row.annotations[column].secondaryStructure;\r
                         }\r
                         else\r
                         {\r
@@ -834,6 +770,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
                         lastSSX[i] = x;\r
                     }\r
                 }\r
+\r
+                yPos++;\r
             }\r
 \r
             x += av.charWidth;\r
@@ -983,16 +921,35 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       }\r
 \r
       eRes = Math.min(eRes, aa.annotations.length);\r
-      for (int j = sRes; j < eRes; j++)\r
+\r
+      int column = sRes;\r
+      int yPos = sRes;\r
+      int aaMax = aa.annotations.length-1;\r
+\r
+      while( yPos < eRes )\r
       {\r
-        if(aa.annotations[j]==null || aa.annotations[j-1]==null)\r
+        if(av.hasHiddenColumns)\r
+        {\r
+          column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+          if(column > aaMax)\r
+          {\r
+            break;\r
+          }\r
+        }\r
+        else\r
+          column = yPos;\r
+\r
+        yPos ++;\r
+\r
+        if(aa.annotations[column]==null || aa.annotations[column-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
+\r
+          g.setColor(aa.annotations[column].colour);\r
+          y1 = y - (int) (((aa.annotations[column-1].value-min) / range) * graphHeight);\r
+          y2 = y - (int) (((aa.annotations[column].value-min) / range) * graphHeight);\r
           g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
           x += av.charWidth;\r
        }\r
@@ -1033,20 +990,35 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
       g.drawLine(x,y2,(eRes-sRes+1)*av.charWidth,y2);\r
 \r
-      eRes = Math.min(eRes, aa.annotations.length-1);\r
 \r
+      int column = sRes;\r
+      int yPos = sRes;\r
+      int aaMax = aa.annotations.length-1;\r
 \r
-      for (int j = sRes; j < eRes; j++)\r
+      while( yPos < eRes )\r
       {\r
+        if(av.hasHiddenColumns)\r
+        {\r
+          column = av.getColumnSelection().adjustForHiddenColumns(yPos);\r
+          if(column > aaMax)\r
+          {\r
+            break;\r
+          }\r
+        }\r
+        else\r
+          column = yPos;\r
+\r
+        yPos ++;\r
 \r
-        if (aa.annotations[j] == null)\r
+        if (aa.annotations[column] == 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
+          g.setColor(aa.annotations[column].colour);\r
+          y1 = y - (int) (((aa.annotations[column].value-min) / (range)) * aa.graphHeight);\r
 \r
           if(y1-y2>0)\r
             g.fillRect(x, y2, av.charWidth, y1-y2 );\r