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2.08, not 2.07
[jalview.git] / src / jalview / gui / AnnotationPanel.java
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index a10d58b..1b4a230 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -57,6 +57,9 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     //Used For mouse Dragging and resizing graphs\r
     int graphStretch = -1;\r
     int graphStretchY = -1;\r
+    int min; //used by mouseDragged to see if user\r
+    int max; //used by mouseDragged to see if user\r
+    boolean mouseDragging = false;\r
 \r
     /**\r
      * Creates a new AnnotationPanel object.\r
@@ -335,34 +338,28 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
         int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
 \r
-        if (evt.isShiftDown())\r
-        {\r
-                /*int start = Integer.parseInt(activeRes.get(activeRes.size() -\r
-                            1).toString());\r
-                int end = res;\r
-\r
-                if (end < start)\r
-                {\r
-                    int temp = end;\r
-                    end = start;\r
-                    start = temp;\r
-                }\r
+        min = res;\r
+        max = res;\r
 \r
-                for (int n = start; n <= end; n++)\r
-                {\r
-                   addEditableColumn(n);\r
-                } */\r
-        }\r
+        if (av.getColumnSelection().contains(res))\r
+          av.getColumnSelection().removeElement(res);\r
         else\r
         {\r
-          if (av.getColumnSelection().contains(res))\r
-            av.getColumnSelection().removeElement(res);\r
-          else\r
             av.getColumnSelection().addElement(res);\r
+            SequenceGroup sg = new SequenceGroup();\r
 \r
-          ap.repaint();\r
+            for (int i = 0; i < av.alignment.getSequences().size(); i++)\r
+            {\r
+                sg.addSequence(av.alignment.getSequenceAt(i), false);\r
+            }\r
 \r
+            sg.setStartRes(res);\r
+            sg.setEndRes(res);\r
+            av.setSelectionGroup(sg);\r
         }\r
+\r
+        ap.repaint();\r
+\r
     }\r
 \r
     /**\r
@@ -374,6 +371,7 @@ public class AnnotationPanel extends JPanel implements MouseListener,
     {\r
       graphStretch = -1;\r
       graphStretchY = -1;\r
+      mouseDragging = false;\r
     }\r
 \r
     /**\r
@@ -383,6 +381,8 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */\r
     public void mouseEntered(MouseEvent evt)\r
     {\r
+      if(mouseDragging)\r
+        ap.seqPanel.scrollCanvas(null);\r
     }\r
 \r
     /**\r
@@ -392,8 +392,11 @@ public class AnnotationPanel extends JPanel implements MouseListener,
      */\r
     public void mouseExited(MouseEvent evt)\r
     {\r
+      if(mouseDragging)\r
+        ap.seqPanel.scrollCanvas(evt);\r
     }\r
 \r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -410,6 +413,56 @@ public class AnnotationPanel extends JPanel implements MouseListener,
         adjustPanelHeight();\r
         ap.repaint();\r
       }\r
+      else\r
+      {\r
+        mouseDragging = true;\r
+\r
+        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();\r
+\r
+        SequenceGroup sg = av.getSelectionGroup();\r
+\r
+        if (res < min)\r
+        {\r
+            min = res;\r
+        }\r
+\r
+        if (res > max)\r
+        {\r
+            max = res;\r
+        }\r
+\r
+        if (sg != null)\r
+        {\r
+            if (!av.getColumnSelection().contains(res))\r
+            {\r
+                av.getColumnSelection().addElement(res);\r
+            }\r
+\r
+            if (res > sg.getStartRes())\r
+            {\r
+                sg.setEndRes(res);\r
+            }\r
+            else if (res < sg.getStartRes())\r
+            {\r
+                sg.setStartRes(res);\r
+            }\r
+\r
+            for (int i = min; i <= max; i++)\r
+            {\r
+                if ((i < sg.getStartRes()) || (i > sg.getEndRes()))\r
+                {\r
+                    av.getColumnSelection().removeElement(i);\r
+                }\r
+                else\r
+                {\r
+                    av.getColumnSelection().addElement(i);\r
+                }\r
+            }\r
+\r
+            ap.repaint();\r
+        }\r
+\r
+      }\r
     }\r
 \r
     /**\r
@@ -905,21 +958,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
       g.setColor(Color.gray);\r
       g.drawLine(x-av.charWidth,y2,(eRes-sRes+1)*av.charWidth,y2);\r
 \r
-\r
-      if(aa.threshold!=null)\r
-      {\r
-          g.setColor(aa.threshold.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.threshold.value-min) / range)*graphHeight);\r
-          g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
-          g2.setStroke(new BasicStroke());\r
-      }\r
-\r
       eRes = Math.min(eRes, aa.annotations.length);\r
 \r
       int column = sRes;\r
@@ -953,6 +991,19 @@ public class AnnotationPanel extends JPanel implements MouseListener,
           g.drawLine(x-av.charWidth/2, y1, x+av.charWidth/2, y2);\r
           x += av.charWidth;\r
        }\r
+       if(aa.threshold!=null)\r
+       {\r
+           g.setColor(aa.threshold.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.threshold.value-min) / range)*graphHeight);\r
+           g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+           g2.setStroke(new BasicStroke());\r
+      }\r
     }\r
 \r
     public void drawBarGraph(Graphics g, AlignmentAnnotation aa,\r
@@ -969,20 +1020,6 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
       float range = max - min;\r
 \r
-      if(aa.threshold!=null)\r
-      {\r
-          g.setColor(aa.threshold.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.threshold.value-min) / range)*aa.graphHeight);\r
-          g.drawLine(x-av.charWidth,y2,(eRes-sRes)*av.charWidth,y2);\r
-          g2.setStroke(new BasicStroke());\r
-      }\r
-\r
       y1 = y2 = y;\r
 \r
       if(min<0)\r
@@ -1029,7 +1066,19 @@ public class AnnotationPanel extends JPanel implements MouseListener,
 \r
           x += av.charWidth;\r
       }\r
+      if(aa.threshold!=null)\r
+      {\r
+          g.setColor(aa.threshold.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.threshold.value-min) / range)*aa.graphHeight);\r
+          g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2);\r
+          g2.setStroke(new BasicStroke());\r
+      }\r
     }\r
 \r
     // used by overview window\r