Alignment properties available

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index d98d5fb..12a2938 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -711,6 +711,48 @@ public class AlignFrame
     {\r
       new FeatureSettings(alignPanel);\r
     }\r
+    else if(source== alProperties)\r
+    {\r
+        StringBuffer contents = new StringBuffer();\r
+\r
+        float avg  = 0;\r
+        int min=Integer.MAX_VALUE, max=0;\r
+        for(int i=0; i<viewport.alignment.getHeight(); i++)\r
+        {\r
+          int size = viewport.alignment.getSequenceAt(i).getEnd()\r
+              -viewport.alignment.getSequenceAt(i).getStart();\r
+          avg += size;\r
+          if(size>max)\r
+            max = size;\r
+          if(size<min)\r
+            min = size;\r
+        }\r
+        avg = avg/(float)viewport.alignment.getHeight();\r
+\r
+        contents.append("\nSequences: "+ viewport.alignment.getHeight());\r
+        contents.append("\nMinimum Sequence Length: "+min);\r
+        contents.append("\nMaximum Sequence Length: "+max);\r
+        contents.append("\nAverage Length: "+(int)avg);\r
+\r
+        if (((Alignment)viewport.alignment).alignmentProperties != null)\r
+        {\r
+          Hashtable props = ((Alignment)viewport.alignment).alignmentProperties;\r
+          Enumeration en = props.keys();\r
+          while(en.hasMoreElements())\r
+          {\r
+            String key = en.nextElement().toString();\r
+            contents.append("\n"+key+"\t"+props.get(key));\r
+          }\r
+        }\r
+\r
+        CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+        cap.setText(contents.toString());\r
+        Frame frame = new Frame();\r
+        frame.add(cap);\r
+        jalview.bin.JalviewLite.addFrame(frame,\r
+                                         "Alignment Properties: "+getTitle()\r
+                                         , 400, 250);\r
+    }\r
     else if (source == overviewMenuItem)\r
     {\r
       overviewMenuItem_actionPerformed();\r
@@ -2289,65 +2331,66 @@ public class AlignFrame
   //////////////////////////////////////////////////////////////////////////////////\r
   //JBuilder Graphics here\r
 \r
-  protected MenuBar alignFrameMenuBar = new MenuBar();\r
-  protected Menu fileMenu = new Menu("File");\r
-  protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
-  protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
-  protected MenuItem loadAnnotations = new MenuItem(\r
+   MenuBar alignFrameMenuBar = new MenuBar();\r
+   Menu fileMenu = new Menu("File");\r
+   MenuItem loadApplication = new MenuItem("View in Full Application");\r
+   MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
+   MenuItem loadAnnotations = new MenuItem(\r
       "Load Features/Annotations ...");\r
-  protected MenuItem outputFeatures = new MenuItem("Export Features ...");\r
-  protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
-\r
-  protected MenuItem closeMenuItem = new MenuItem("Close");\r
-  protected Menu editMenu = new Menu("Edit");\r
-  protected Menu viewMenu = new Menu("View");\r
-  protected Menu colourMenu = new Menu("Colour");\r
-  protected Menu calculateMenu = new Menu("Calculate");\r
-  protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
-  protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
-  protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
-  protected MenuItem remove2LeftMenuItem = new MenuItem();\r
-  protected MenuItem remove2RightMenuItem = new MenuItem();\r
-  protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
-  protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
-  protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
-  protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
-  protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
-  protected MenuItem sortIDMenuItem = new MenuItem();\r
-  protected MenuItem sortGroupMenuItem = new MenuItem();\r
-  protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
-  protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
-  protected MenuItem PCAMenuItem = new MenuItem();\r
-  protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
-  protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
+   MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+   MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
+   MenuItem closeMenuItem = new MenuItem("Close");\r
+   Menu editMenu = new Menu("Edit");\r
+   Menu viewMenu = new Menu("View");\r
+   Menu colourMenu = new Menu("Colour");\r
+   Menu calculateMenu = new Menu("Calculate");\r
+   MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+   MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+   MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
+   MenuItem remove2LeftMenuItem = new MenuItem();\r
+   MenuItem remove2RightMenuItem = new MenuItem();\r
+   MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+   MenuItem removeAllGapsMenuItem = new MenuItem();\r
+   CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+   CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+   MenuItem sortPairwiseMenuItem = new MenuItem();\r
+   MenuItem sortIDMenuItem = new MenuItem();\r
+   MenuItem sortGroupMenuItem = new MenuItem();\r
+   MenuItem removeRedundancyMenuItem = new MenuItem();\r
+   MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+   MenuItem PCAMenuItem = new MenuItem();\r
+   MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+   MenuItem neighbourTreeMenuItem = new MenuItem();\r
   BorderLayout borderLayout1 = new BorderLayout();\r
   public Label statusBar = new Label();\r
-  protected Menu outputTextboxMenu = new Menu();\r
-  protected MenuItem clustalColour = new MenuItem();\r
-  protected MenuItem zappoColour = new MenuItem();\r
-  protected MenuItem taylorColour = new MenuItem();\r
-  protected MenuItem hydrophobicityColour = new MenuItem();\r
-  protected MenuItem helixColour = new MenuItem();\r
-  protected MenuItem strandColour = new MenuItem();\r
-  protected MenuItem turnColour = new MenuItem();\r
-  protected MenuItem buriedColour = new MenuItem();\r
-  protected MenuItem userDefinedColour = new MenuItem();\r
-  protected MenuItem PIDColour = new MenuItem();\r
-  protected MenuItem BLOSUM62Colour = new MenuItem();\r
+   Menu outputTextboxMenu = new Menu();\r
+   MenuItem clustalColour = new MenuItem();\r
+   MenuItem zappoColour = new MenuItem();\r
+   MenuItem taylorColour = new MenuItem();\r
+   MenuItem hydrophobicityColour = new MenuItem();\r
+   MenuItem helixColour = new MenuItem();\r
+   MenuItem strandColour = new MenuItem();\r
+   MenuItem turnColour = new MenuItem();\r
+   MenuItem buriedColour = new MenuItem();\r
+   MenuItem userDefinedColour = new MenuItem();\r
+   MenuItem PIDColour = new MenuItem();\r
+   MenuItem BLOSUM62Colour = new MenuItem();\r
   MenuItem njTreeBlosumMenuItem = new MenuItem();\r
   MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
-  protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
-  protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+   CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+   CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+   MenuItem alProperties = new MenuItem("Alignment Properties...");\r
   MenuItem overviewMenuItem = new MenuItem();\r
-  protected MenuItem undoMenuItem = new MenuItem();\r
-  protected MenuItem redoMenuItem = new MenuItem();\r
-  protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+   MenuItem undoMenuItem = new MenuItem();\r
+   MenuItem redoMenuItem = new MenuItem();\r
+   CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
   MenuItem noColourmenuItem = new MenuItem();\r
-  protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
-  protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+   CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+   CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
   MenuItem findMenuItem = new MenuItem();\r
-  protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
-  protected MenuItem nucleotideColour = new MenuItem();\r
+   CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+   MenuItem nucleotideColour = new MenuItem();\r
   MenuItem deleteGroups = new MenuItem();\r
   MenuItem delete = new MenuItem();\r
   MenuItem copy = new MenuItem();\r
@@ -2355,23 +2398,23 @@ public class AlignFrame
   Menu pasteMenu = new Menu();\r
   MenuItem pasteNew = new MenuItem();\r
   MenuItem pasteThis = new MenuItem();\r
-  protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
-  protected MenuItem font = new MenuItem();\r
-  protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
-  protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
-  protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+   CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+   MenuItem font = new MenuItem();\r
+   CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+   CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+   CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
   MenuItem modifyPID = new MenuItem();\r
   MenuItem modifyConservation = new MenuItem();\r
-  protected CheckboxMenuItem autoCalculate\r
+   CheckboxMenuItem autoCalculate\r
       = new CheckboxMenuItem("Autocalculate Consensus", true);\r
-  protected Menu sortByTreeMenu = new Menu();\r
+   Menu sortByTreeMenu = new Menu();\r
   Menu sort = new Menu();\r
   Menu calculate = new Menu();\r
   MenuItem inputText = new MenuItem();\r
   Menu helpMenu = new Menu();\r
   MenuItem documentation = new MenuItem();\r
   MenuItem about = new MenuItem();\r
-  protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+   CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
   Panel embeddedMenu;\r
   Label embeddedEdit;\r
   Label embeddedSelect;\r
@@ -2485,6 +2528,7 @@ public class AlignFrame
     annotationPanelMenuItem.addItemListener(this);\r
     colourTextMenuItem.setLabel("Colour Text");\r
     colourTextMenuItem.addItemListener(this);\r
+    alProperties.addActionListener(this);\r
     overviewMenuItem.setLabel("Overview Window");\r
     overviewMenuItem.addActionListener(this);\r
     undoMenuItem.setEnabled(false);\r
@@ -2630,6 +2674,8 @@ public class AlignFrame
     viewMenu.add(sequenceFeatures);\r
     viewMenu.add(featureSettings);\r
     viewMenu.addSeparator();\r
+    viewMenu.add(alProperties);\r
+    viewMenu.addSeparator();\r
     viewMenu.add(overviewMenuItem);\r
     colourMenu.add(applyToAllGroups);\r
     colourMenu.addSeparator();\r