Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

[jalview.git] / src / jalview / appletgui / AlignFrame.java

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 14b3e6a..cfd3d00 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -52,6 +52,8 @@ import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FeaturesFile;
 import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.TCoffeeScoreFile;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -62,6 +64,7 @@ import jalview.schemes.HydrophobicColourScheme;
 import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.RNAHelicesColour;
 import jalview.schemes.RNAHelicesColourChooser;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
@@ -1256,7 +1259,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // }
     else if (source == RNAHelixColour)
     {
-      new RNAHelicesColourChooser(viewport, alignPanel);
+      changeColour(new RNAHelicesColour(viewport.getAlignment()));
+      // new RNAHelicesColourChooser(viewport, alignPanel);
     }
     else if (source == modifyPID)
     {
@@ -1363,7 +1367,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             "label.alignment_output_command",
             new Object[] { e.getActionCommand() }), 600, 500);
 
-    FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
+    FileFormatI fileFormat = FileFormats.getInstance().forName(
+            e.getActionCommand());
     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
             fileFormat, viewport.getAlignment(),
             viewport.getShowJVSuffix()));
@@ -1481,10 +1486,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       url.append(appendProtocol(viewport.applet.getParameter("annotations")));
     }
 
-    if (viewport.applet.getParameter("jnetfile") != null)
+    if (viewport.applet.getParameter("jnetfile") != null
+            || viewport.applet.getParameter("jpredfile") != null)
     {
       url.append("&annotations=");
-      url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
+      url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
+              .getParameter("jnetfile") : viewport.applet
+              .getParameter("jpredfile")));
     }
 
     if (viewport.applet.getParameter("defaultColour") != null)
@@ -2673,26 +2681,43 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   protected void conservationMenuItem_actionPerformed()
   {
-    viewport.setConservationSelected(conservationMenuItem.getState());
+    boolean selected = conservationMenuItem.getState();
+    modifyConservation.setEnabled(selected);
+    viewport.setConservationSelected(selected);
 
-    viewport.setAbovePIDThreshold(false);
-    abovePIDThreshold.setState(false);
+    // viewport.setAbovePIDThreshold(false);
+    // abovePIDThreshold.setState(false);
 
     changeColour(viewport.getGlobalColourScheme());
 
-    modifyConservation_actionPerformed();
+    if (selected)
+    {
+      modifyConservation_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hideConservationSlider();
+    }
   }
 
   public void abovePIDThreshold_actionPerformed()
   {
-    viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
-
-    conservationMenuItem.setState(false);
-    viewport.setConservationSelected(false);
+    boolean selected = abovePIDThreshold.getState();
+    modifyPID.setEnabled(selected);
+    viewport.setAbovePIDThreshold(selected);
+    // conservationMenuItem.setState(false);
+    // viewport.setConservationSelected(false);
 
     changeColour(viewport.getGlobalColourScheme());
 
-    modifyPID_actionPerformed();
+    if (selected)
+    {
+      modifyPID_actionPerformed();
+    }
+    else
+    {
+      SliderPanel.hidePIDSlider();
+    }
   }
 
   public void sortPairwiseMenuItem_actionPerformed()
@@ -3237,7 +3262,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     inputText.addActionListener(this);
     Menu outputTextboxMenu = new Menu(
             MessageManager.getString("label.out_to_textbox"));
-    for (String ff : FileFormat.getWritableFormats(true))
+    for (String ff : FileFormats.getInstance().getWritableFormats(true))
     {
       MenuItem item = new MenuItem(ff);
 
@@ -3460,45 +3485,50 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getString("label.apply_colour_to_all_groups"));
     applyToAllGroups.setState(true);
     applyToAllGroups.addItemListener(this);
-    clustalColour.setLabel(MessageManager.getString("label.clustalx"));
+    clustalColour.setLabel(MessageManager
+            .getString("label.colourScheme_clustal"));
     clustalColour.addActionListener(this);
-    zappoColour.setLabel(MessageManager.getString("label.zappo"));
+    zappoColour.setLabel(MessageManager
+            .getString("label.colourScheme_zappo"));
     zappoColour.addActionListener(this);
-    taylorColour.setLabel(MessageManager.getString("label.taylor"));
+    taylorColour.setLabel(MessageManager
+            .getString("label.colourScheme_taylor"));
     taylorColour.addActionListener(this);
     hydrophobicityColour.setLabel(MessageManager
-            .getString("label.hydrophobicity"));
+            .getString("label.colourScheme_hydrophobic"));
     hydrophobicityColour.addActionListener(this);
-    helixColour
-            .setLabel(MessageManager.getString("label.helix_propensity"));
+    helixColour.setLabel(MessageManager
+            .getString("label.colourScheme_helix_propensity"));
     helixColour.addActionListener(this);
     strandColour.setLabel(MessageManager
-            .getString("label.strand_propensity"));
+            .getString("label.colourScheme_strand_propensity"));
     strandColour.addActionListener(this);
-    turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
+    turnColour.setLabel(MessageManager
+            .getString("label.colourScheme_turn_propensity"));
     turnColour.addActionListener(this);
-    buriedColour.setLabel(MessageManager.getString("label.buried_index"));
+    buriedColour.setLabel(MessageManager
+            .getString("label.colourScheme_buried_index"));
     buriedColour.addActionListener(this);
     purinePyrimidineColour.setLabel(MessageManager
-            .getString("label.purine_pyrimidine"));
+            .getString("label.colourScheme_purine/pyrimidine"));
     purinePyrimidineColour.addActionListener(this);
     // RNAInteractionColour.setLabel(MessageManager
     // .getString("label.rna_interaction"));
     // RNAInteractionColour.addActionListener(this);
     RNAHelixColour.setLabel(MessageManager
-            .getString("action.by_rna_helixes"));
+            .getString("label.colourScheme_rna_helices"));
     RNAHelixColour.addActionListener(this);
     userDefinedColour.setLabel(MessageManager
             .getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
     PIDColour.setLabel(MessageManager
-            .getString("label.percentage_identity"));
+            .getString("label.colourScheme_%_identity"));
     PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel(MessageManager
-            .getString("label.blosum62_score"));
+            .getString("label.colourScheme_blosum62"));
     BLOSUM62Colour.addActionListener(this);
-    tcoffeeColour
-            .setLabel(MessageManager.getString("label.tcoffee_scores"));
+    tcoffeeColour.setLabel(MessageManager
+            .getString("label.colourScheme_t-coffee_scores"));
     // it will be enabled only if a score file is provided
     tcoffeeColour.setEnabled(false);
     tcoffeeColour.addActionListener(this);
@@ -3510,13 +3540,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     abovePIDThreshold.setLabel(MessageManager
             .getString("label.above_identity_threshold"));
     abovePIDThreshold.addItemListener(this);
-    nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
+    nucleotideColour.setLabel(MessageManager
+            .getString("label.colourScheme_nucleotide"));
     nucleotideColour.addActionListener(this);
     modifyPID.setLabel(MessageManager
             .getString("label.modify_identity_threshold"));
+    modifyPID.setEnabled(abovePIDThreshold.getState());
     modifyPID.addActionListener(this);
     modifyConservation.setLabel(MessageManager
             .getString("label.modify_conservation_threshold"));
+    modifyConservation.setEnabled(conservationMenuItem.getState());
     modifyConservation.addActionListener(this);
     annotationColour.setLabel(MessageManager
             .getString("action.by_annotation"));
@@ -3550,7 +3583,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             .getString("label.neighbour_joining_identity"));
     neighbourTreeMenuItem.addActionListener(this);
     avDistanceTreeBlosumMenuItem.setLabel(MessageManager
-            .getString("label.average_distance_bloslum62"));
+            .getString("label.average_distance_blosum62"));
     avDistanceTreeBlosumMenuItem.addActionListener(this);
     njTreeBlosumMenuItem.setLabel(MessageManager
             .getString("label.neighbour_blosum62"));