X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;fp=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=941052de099e9c6bbf2a81d88fe4b2d9d01a011e;hb=e23c8a1df90ccbb262f477a1b6c4b49808da80ff;hp=f126d55ba0845fba540725b0fe5dae7a26e124f2;hpb=902a15eeb7361608e4b0b8b421a5435d21b1ee63;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index f126d55..941052d 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -42,8 +42,10 @@ import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ClustalxColourScheme; import jalview.schemes.CollectionColourScheme; +import jalview.schemes.CollectionColourSchemeI; import jalview.schemes.HelixColourScheme; import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.JalviewColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; @@ -79,33 +81,37 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem editGroupName = new MenuItem(); - protected MenuItem clustalColour = new MenuItem(); + CheckboxMenuItem noColour = new CheckboxMenuItem(); - protected MenuItem zappoColour = new MenuItem(); + protected CheckboxMenuItem clustalColour = new CheckboxMenuItem(); - protected MenuItem taylorColour = new MenuItem(); + protected CheckboxMenuItem zappoColour = new CheckboxMenuItem(); - protected MenuItem hydrophobicityColour = new MenuItem(); + protected CheckboxMenuItem taylorColour = new CheckboxMenuItem(); - protected MenuItem helixColour = new MenuItem(); + protected CheckboxMenuItem hydrophobicityColour = new CheckboxMenuItem(); - protected MenuItem strandColour = new MenuItem(); + protected CheckboxMenuItem helixColour = new CheckboxMenuItem(); - protected MenuItem turnColour = new MenuItem(); + protected CheckboxMenuItem strandColour = new CheckboxMenuItem(); - protected MenuItem buriedColour = new MenuItem(); + protected CheckboxMenuItem turnColour = new CheckboxMenuItem(); - protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem(); + protected CheckboxMenuItem buriedColour = new CheckboxMenuItem(); - protected MenuItem userDefinedColour = new MenuItem(); + protected CheckboxMenuItem PIDColour = new CheckboxMenuItem(); - protected MenuItem PIDColour = new MenuItem(); + protected CheckboxMenuItem BLOSUM62Colour = new CheckboxMenuItem(); - protected MenuItem BLOSUM62Colour = new MenuItem(); + CheckboxMenuItem nucleotideColour = new CheckboxMenuItem(); - MenuItem noColourmenuItem = new MenuItem(); + CheckboxMenuItem purinePyrimidineColour = new CheckboxMenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + protected MenuItem userDefinedColour = new MenuItem(); + + protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem(); + + protected CheckboxMenuItem conservationColour = new CheckboxMenuItem(); final AlignmentPanel ap; @@ -113,10 +119,6 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem createGroupMenuItem = new MenuItem(); - MenuItem nucleotideMenuItem = new MenuItem(); - - MenuItem purinePyrimidineMenuItem = new MenuItem(); - Menu colourMenu = new Menu(); CheckboxMenuItem showBoxes = new CheckboxMenuItem(); @@ -249,8 +251,13 @@ public class APopupMenu extends java.awt.PopupMenu implements { menu1.setLabel(MessageManager.getString("action.edit_group")); groupMenu.remove(createGroupMenuItem); + if (sg.cs != null) + { + abovePIDColour.setState(sg.cs.getThreshold() > 0); + conservationColour.setState(sg.cs.conservationApplied()); + } } - + setSelectedColour(sg.cs); } else { @@ -308,6 +315,36 @@ public class APopupMenu extends java.awt.PopupMenu implements } /** + * Select the menu item (if any) matching the current colour scheme. This + * works by matching the menu item name (not display text) to the canonical + * name of the colour scheme. + * + * @param cs + */ + protected void setSelectedColour(CollectionColourSchemeI cs) + { + if (cs == null || cs.getColourScheme() == null) + { + noColour.setState(true); + } + else + { + String name = cs.getColourScheme().getSchemeName(); + for (int i = 0; i < colourMenu.getItemCount(); i++) + { + MenuItem item = colourMenu.getItem(i); + if (item instanceof CheckboxMenuItem) + { + if (name.equals(item.getName())) + { + ((CheckboxMenuItem) item).setState(true); + } + } + } + } + } + + /** * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided. * * @param seq @@ -502,38 +539,28 @@ public class APopupMenu extends java.awt.PopupMenu implements linkMenu.add(item); } + /** + * Actions on selecting / unselecting a checkbox menu item + */ @Override public void itemStateChanged(ItemEvent evt) { - if (evt.getSource() == abovePIDColour) - { - abovePIDColour_itemStateChanged(); - } - else if (evt.getSource() == showColourText) - { - showColourText_itemStateChanged(); - } - else if (evt.getSource() == showText) + Object source = evt.getSource(); + if (source == noColour) { - showText_itemStateChanged(); + noColourmenuItem_actionPerformed(); } - else if (evt.getSource() == showBoxes) + else if (source == clustalColour) { - showBoxes_itemStateChanged(); + clustalColour_actionPerformed(); } - else if (evt.getSource() == displayNonconserved) + else if (source == BLOSUM62Colour) { - this.showNonconserved_itemStateChanged(); + BLOSUM62Colour_actionPerformed(); } - } - - @Override - public void actionPerformed(ActionEvent evt) - { - Object source = evt.getSource(); - if (source == clustalColour) + else if (evt.getSource() == PIDColour) { - clustalColour_actionPerformed(); + PIDColour_actionPerformed(); } else if (source == zappoColour) { @@ -563,34 +590,50 @@ public class APopupMenu extends java.awt.PopupMenu implements { buriedColour_actionPerformed(); } - else if (source == nucleotideMenuItem) + else if (source == nucleotideColour) { nucleotideMenuItem_actionPerformed(); } - else if (source == purinePyrimidineMenuItem) + else if (source == purinePyrimidineColour) { purinePyrimidineColour_actionPerformed(); } - - else if (source == userDefinedColour) + else if (source == abovePIDColour) { - userDefinedColour_actionPerformed(); + abovePIDColour_itemStateChanged(); } - else if (source == PIDColour) + else if (source == conservationColour) { - PIDColour_actionPerformed(); + conservationMenuItem_itemStateChanged(); } - else if (source == BLOSUM62Colour) + else if (source == showColourText) { - BLOSUM62Colour_actionPerformed(); + showColourText_itemStateChanged(); } - else if (source == noColourmenuItem) + else if (source == showText) { - noColourmenuItem_actionPerformed(); + showText_itemStateChanged(); } - else if (source == conservationMenuItem) + else if (source == showBoxes) { - conservationMenuItem_itemStateChanged(); + showBoxes_itemStateChanged(); + } + else if (source == displayNonconserved) + { + this.showNonconserved_itemStateChanged(); + } + } + + /** + * Actions on clicking a menu item + */ + @Override + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + if (source == userDefinedColour) + { + userDefinedColour_actionPerformed(); } else if (source == unGroupMenuItem) { @@ -939,7 +982,7 @@ public class APopupMenu extends java.awt.PopupMenu implements groupMenu.add(unGroupMenuItem); groupMenu.add(menu1); - colourMenu.add(noColourmenuItem); + colourMenu.add(noColour); colourMenu.add(clustalColour); colourMenu.add(BLOSUM62Colour); colourMenu.add(PIDColour); @@ -950,62 +993,80 @@ public class APopupMenu extends java.awt.PopupMenu implements colourMenu.add(strandColour); colourMenu.add(turnColour); colourMenu.add(buriedColour); - colourMenu.add(nucleotideMenuItem); - colourMenu.add(purinePyrimidineMenuItem); + colourMenu.add(nucleotideColour); + colourMenu.add(purinePyrimidineColour); colourMenu.add(userDefinedColour); colourMenu.addSeparator(); colourMenu.add(abovePIDColour); - colourMenu.add(conservationMenuItem); + colourMenu.add(conservationColour); - noColourmenuItem.setLabel(MessageManager.getString("label.none")); - noColourmenuItem.addActionListener(this); + noColour.setLabel(MessageManager.getString("label.none")); + noColour.addItemListener(this); + /* + * setName allows setSelectedColour to do its thing + */ clustalColour.setLabel(MessageManager .getString("label.colourScheme_clustal")); - clustalColour.addActionListener(this); + clustalColour.setName(JalviewColourScheme.Clustal.toString()); + clustalColour.addItemListener(this); + BLOSUM62Colour.setLabel(MessageManager + .getString("label.colourScheme_blosum62")); + BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString()); + BLOSUM62Colour.addItemListener(this); + PIDColour.setLabel(MessageManager + .getString("label.colourScheme_%_identity")); + PIDColour.setName(JalviewColourScheme.PID.toString()); + PIDColour.addItemListener(this); zappoColour.setLabel(MessageManager .getString("label.colourScheme_zappo")); - zappoColour.addActionListener(this); + zappoColour.setName(JalviewColourScheme.Zappo.toString()); + zappoColour.addItemListener(this); taylorColour.setLabel(MessageManager .getString("label.colourScheme_taylor")); - taylorColour.addActionListener(this); + taylorColour.setName(JalviewColourScheme.Taylor.toString()); + taylorColour.addItemListener(this); hydrophobicityColour.setLabel(MessageManager .getString("label.colourScheme_hydrophobic")); - hydrophobicityColour.addActionListener(this); + hydrophobicityColour + .setName(JalviewColourScheme.Hydrophobic.toString()); + hydrophobicityColour.addItemListener(this); helixColour.setLabel(MessageManager .getString("label.colourScheme_helix_propensity")); - helixColour.addActionListener(this); + helixColour.setName(JalviewColourScheme.Helix.toString()); + helixColour.addItemListener(this); strandColour.setLabel(MessageManager .getString("label.colourScheme_strand_propensity")); - strandColour.addActionListener(this); + strandColour.setName(JalviewColourScheme.Strand.toString()); + strandColour.addItemListener(this); turnColour.setLabel(MessageManager .getString("label.colourScheme_turn_propensity")); - turnColour.addActionListener(this); + turnColour.setName(JalviewColourScheme.Turn.toString()); + turnColour.addItemListener(this); buriedColour.setLabel(MessageManager .getString("label.colourScheme_buried_index")); - buriedColour.addActionListener(this); - abovePIDColour.setLabel(MessageManager - .getString("label.above_identity_threshold")); + buriedColour.setName(JalviewColourScheme.Buried.toString()); + buriedColour.addItemListener(this); + nucleotideColour.setLabel(MessageManager + .getString("label.colourScheme_nucleotide")); + nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString()); + nucleotideColour.addItemListener(this); + purinePyrimidineColour.setLabel(MessageManager + .getString("label.colourScheme_purine/pyrimidine")); + purinePyrimidineColour.setName(JalviewColourScheme.PurinePyrimidine + .toString()); + purinePyrimidineColour.addItemListener(this); userDefinedColour.setLabel(MessageManager .getString("action.user_defined")); userDefinedColour.addActionListener(this); - PIDColour.setLabel(MessageManager - .getString("label.colourScheme_%_identity")); - PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel(MessageManager - .getString("label.colourScheme_blosum62")); - BLOSUM62Colour.addActionListener(this); - conservationMenuItem.setLabel(MessageManager - .getString("label.conservation")); - nucleotideMenuItem.setLabel(MessageManager - .getString("label.colourScheme_nucleotide")); - nucleotideMenuItem.addActionListener(this); - purinePyrimidineMenuItem.setLabel(MessageManager - .getString("label.colourScheme_purine/pyrimidine")); - purinePyrimidineMenuItem.addActionListener(this); - conservationMenuItem.addItemListener(this); + + abovePIDColour.setLabel(MessageManager + .getString("label.above_identity_threshold")); abovePIDColour.addItemListener(this); + conservationColour.setLabel(MessageManager + .getString("label.conservation")); + conservationColour.addItemListener(this); editMenu.add(copy); copy.addActionListener(this); @@ -1185,9 +1246,10 @@ public class APopupMenu extends java.awt.PopupMenu implements return; } - if (conservationMenuItem.getState()) + if (conservationColour.getState()) { - Conservation conservation = Conservation.calculateConservation("Group", sg + Conservation conservation = Conservation.calculateConservation( + "Group", sg .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av .getAlignment().getWidth(), false, ap.av.getConsPercGaps(), false);