import jalview.analysis.AlignmentAnnotationUtils;
import jalview.analysis.AlignmentUtils;
import jalview.analysis.Conservation;
+import jalview.bin.JalviewLite;
import jalview.commands.ChangeCaseCommand;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShader;
+import jalview.renderer.ResidueShaderI;
import jalview.schemes.Blosum62ColourScheme;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.JalviewColourScheme;
import jalview.schemes.NucleotideColourScheme;
import jalview.schemes.PIDColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
import jalview.schemes.StrandColourScheme;
import jalview.schemes.TaylorColourScheme;
import jalview.schemes.TurnColourScheme;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
+import java.util.SortedMap;
import java.util.TreeMap;
import java.util.Vector;
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 CheckboxMenuItem PIDColour = new CheckboxMenuItem();
+
+ protected CheckboxMenuItem BLOSUM62Colour = new CheckboxMenuItem();
+
+ CheckboxMenuItem nucleotideColour = new CheckboxMenuItem();
+
+ CheckboxMenuItem purinePyrimidineColour = new CheckboxMenuItem();
protected MenuItem userDefinedColour = new MenuItem();
- protected MenuItem PIDColour = new MenuItem();
+ protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
- protected MenuItem BLOSUM62Colour = new MenuItem();
+ MenuItem modifyPID = new MenuItem();
- MenuItem noColourmenuItem = new MenuItem();
+ protected CheckboxMenuItem conservationColour = new CheckboxMenuItem();
+
+ MenuItem modifyConservation = new MenuItem();
- protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
+ MenuItem noColourmenuItem = new MenuItem();
final AlignmentPanel ap;
MenuItem createGroupMenuItem = new MenuItem();
- MenuItem nucleotideMenuItem = new MenuItem();
-
Menu colourMenu = new Menu();
CheckboxMenuItem showBoxes = new CheckboxMenuItem();
Menu menu1 = new Menu();
public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
- Vector<String> links)
+ List<String> links)
{
// /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
e.printStackTrace();
}
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
- MenuItem item = new MenuItem(
- jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+ MenuItem item = new MenuItem(ff);
item.addActionListener(this);
outputmenu.add(item);
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg != null && sg.getSize() > 0)
{
+ if (sg.isNucleotide())
+ {
+ conservationColour.setEnabled(false);
+ clustalColour.setEnabled(false);
+ BLOSUM62Colour.setEnabled(false);
+ zappoColour.setEnabled(false);
+ taylorColour.setEnabled(false);
+ hydrophobicityColour.setEnabled(false);
+ helixColour.setEnabled(false);
+ strandColour.setEnabled(false);
+ turnColour.setEnabled(false);
+ buriedColour.setEnabled(false);
+ }
+ else
+ {
+ purinePyrimidineColour.setEnabled(false);
+ nucleotideColour.setEnabled(false);
+ }
editGroupName.setLabel(MessageManager.formatMessage(
"label.name_param", new Object[] { sg.getName() }));
showText.setState(sg.getDisplayText());
{
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());
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
+ }
}
-
+ setSelectedColour(sg.cs);
}
else
{
if (links != null && links.size() > 0)
{
- Menu linkMenu = new Menu(MessageManager.getString("action.link"));
- for (int i = 0; i < links.size(); i++)
- {
- String link = links.elementAt(i);
- UrlLink urlLink = new UrlLink(link);
- if (!urlLink.isValid())
- {
- System.err.println(urlLink.getInvalidMessage());
- continue;
- }
- final String target = urlLink.getTarget(); // link.substring(0,
- // link.indexOf("|"));
- final String label = urlLink.getLabel();
- if (seq != null && urlLink.isDynamic())
- {
-
- // collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRefs(), new String[] { target });
- // collect id string too
- String id = seq.getName();
- String descr = seq.getDescription();
- if (descr != null && descr.length() < 1)
- {
- descr = null;
- }
- if (dbr != null)
- {
- for (int r = 0; r < dbr.length; r++)
- {
- if (id != null && dbr[r].getAccessionId().equals(id))
- {
- // suppress duplicate link creation for the bare sequence ID
- // string with this link
- id = null;
- }
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
- true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
- }
- }
- }
- }
- if (id != null)
- {
- // create Bare ID link for this RUL
- String[] urls = urlLink.makeUrls(id, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- // addshowLink(linkMenu, target, url_pref + id + url_suff);
- }
- // Now construct URLs from description but only try to do it for regex
- // URL links
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description only if regex matches
- String[] urls = urlLink.makeUrls(descr, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- else
- {
- addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
- }
- /*
- * final String url;
- *
- * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
- * string and any matching database reference accessions String url_pref
- * = link.substring(link.indexOf("|") + 1,
- * link.indexOf("$SEQUENCE_ID$"));
- *
- * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
- * // collect matching db-refs DBRefEntry[] dbr =
- * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
- * String[]{target}); // collect id string too String id =
- * seq.getName(); if (id.indexOf("|") > -1) { id =
- * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
- * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
- * suppress duplicate link creation for the bare sequence ID string with
- * this link id = null; } addshowLink(linkMenu,
- * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
- * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
- * create Bare ID link for this RUL addshowLink(linkMenu, target,
- * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
- * link.substring(link.lastIndexOf("|")+1)); }
- */
- }
- if (linkMenu.getItemCount() > 0)
- {
- if (seq != null)
- {
- seqMenu.add(linkMenu);
- }
- else
- {
- add(linkMenu);
- }
- }
+ addFeatureLinks(seq, links);
}
+
// TODO: add group link menu entry here
if (seq != null)
{
}
/**
+ * 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(ResidueShaderI 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
+ * @param links
+ */
+ void addFeatureLinks(final SequenceI seq, List<String> links)
+ {
+ Menu linkMenu = new Menu(MessageManager.getString("action.link"));
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+
+ for (String link : links)
+ {
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ System.err.println("Exception for URLLink '" + link + "': "
+ + foo.getMessage());
+ continue;
+ }
+
+ if (!urlLink.isValid())
+ {
+ System.err.println(urlLink.getInvalidMessage());
+ continue;
+ }
+
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
+
+ addshowLinks(linkMenu, linkset.values());
+
+ // disable link menu if there are no valid entries
+ if (linkMenu.getItemCount() > 0)
+ {
+ linkMenu.setEnabled(true);
+ }
+ else
+ {
+ linkMenu.setEnabled(false);
+ }
+
+ if (seq != null)
+ {
+ seqMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+
+ }
+
+ private void addshowLinks(Menu linkMenu, Collection<List<String>> linkset)
+ {
+ for (List<String> linkstrset : linkset)
+ {
+ // split linkstr into label and url
+ addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
+ }
+ }
+
+ /**
* Build menus for annotation types that may be shown or hidden, and for
* 'reference annotations' that may be added to the alignment.
*/
* Temporary store to hold distinct calcId / type pairs for the tooltip.
* Using TreeMap means calcIds are shown in alphabetical order.
*/
- Map<String, String> tipEntries = new TreeMap<String, String>();
+ SortedMap<String, String> tipEntries = new TreeMap<String, String>();
final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
AlignmentI al = this.ap.av.getAlignment();
AlignmentUtils.findAddableReferenceAnnotations(forSequences,
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)
{
{
buriedColour_actionPerformed();
}
- else if (source == nucleotideMenuItem)
+ else if (source == nucleotideColour)
{
nucleotideMenuItem_actionPerformed();
}
-
- else if (source == userDefinedColour)
+ else if (source == purinePyrimidineColour)
{
- userDefinedColour_actionPerformed();
+ purinePyrimidineColour_actionPerformed();
}
- else if (source == PIDColour)
+ else if (source == abovePIDColour)
{
- PIDColour_actionPerformed();
+ abovePIDColour_itemStateChanged();
}
- else if (source == BLOSUM62Colour)
+ else if (source == conservationColour)
{
- BLOSUM62Colour_actionPerformed();
+ conservationMenuItem_itemStateChanged();
}
- else if (source == noColourmenuItem)
+ else if (source == showColourText)
{
- noColourmenuItem_actionPerformed();
+ showColourText_itemStateChanged();
+ }
+ else if (source == showText)
+ {
+ showText_itemStateChanged();
+ }
+ else if (source == showBoxes)
+ {
+ 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 == conservationMenuItem)
+ else if (source == modifyConservation)
{
conservationMenuItem_itemStateChanged();
}
+ else if (source == modifyPID)
+ {
+ abovePIDColour_itemStateChanged();
+ }
else if (source == unGroupMenuItem)
{
unGroupMenuItem_actionPerformed();
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.selection_output_command",
new Object[] { e.getActionCommand() }), 600, 500);
// JBPNote: getSelectionAsNewSequence behaviour has changed - this method
// now returns a full copy of sequence data
// TODO consider using getSequenceSelection instead here
- cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
- e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true));
+ FileFormatI fileFormat = FileFormats.getInstance().forName(
+ e.getActionCommand());
+ cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
+ ap.av.getShowJVSuffix(), ap, true));
}
CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
- StringBuffer contents = new StringBuffer();
+ StringBuilder contents = new StringBuilder(128);
for (SequenceI seq : sequences)
{
contents.append(MessageManager.formatMessage(
seq,
true,
true,
- false,
(ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
.getMinMax() : null);
contents.append("</p>");
void addPDB()
{
- if (seq.getAllPDBEntries() != null)
+ Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
+ if (pdbs != null && !pdbs.isEmpty())
{
- PDBEntry entry = seq.getAllPDBEntries().firstElement();
+ PDBEntry entry = pdbs.firstElement();
if (ap.av.applet.jmolAvailable)
{
- new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
- null, ap, AppletFormatAdapter.URL);
+ new AppletJmol(entry, new SequenceI[] { seq }, null, ap,
+ DataSourceType.URL);
}
else
{
new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
- ap, AppletFormatAdapter.URL);
+ ap, DataSourceType.URL);
}
}
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
"label.paste_pdb_file_for_sequence",
new Object[] { seq.getName() }), 400, 300);
}
.getString("action.create_group"));
createGroupMenuItem.addActionListener(this);
- nucleotideMenuItem.setLabel(MessageManager
- .getString("label.nucleotide"));
- nucleotideMenuItem.addActionListener(this);
- conservationMenuItem.addItemListener(this);
- abovePIDColour.addItemListener(this);
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
colourMenu.setLabel(MessageManager.getString("label.group_colour"));
showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
sequenceDetails.addActionListener(this);
selSeqDetails.addActionListener(this);
displayNonconserved.setLabel(MessageManager
- .getString("label.show_non_conversed"));
+ .getString("label.show_non_conserved"));
displayNonconserved.setState(false);
displayNonconserved.addItemListener(this);
showText.setLabel(MessageManager.getString("action.text"));
groupMenu.add(unGroupMenuItem);
groupMenu.add(menu1);
- colourMenu.add(noColourmenuItem);
+ colourMenu.add(noColour);
colourMenu.add(clustalColour);
colourMenu.add(BLOSUM62Colour);
colourMenu.add(PIDColour);
colourMenu.add(strandColour);
colourMenu.add(turnColour);
colourMenu.add(buriedColour);
- colourMenu.add(nucleotideMenuItem);
+ colourMenu.add(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
colourMenu.add(userDefinedColour);
colourMenu.addSeparator();
+ colourMenu.add(conservationColour);
+ colourMenu.add(modifyConservation);
colourMenu.add(abovePIDColour);
- colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyPID);
- 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.clustalx_colours"));
- clustalColour.addActionListener(this);
- zappoColour.setLabel(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(this);
- taylorColour.setLabel(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(this);
+ .getString("label.colourScheme_clustal"));
+ 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.setName(JalviewColourScheme.Zappo.toString());
+ zappoColour.addItemListener(this);
+ taylorColour.setLabel(MessageManager
+ .getString("label.colourScheme_taylor"));
+ taylorColour.setName(JalviewColourScheme.Taylor.toString());
+ taylorColour.addItemListener(this);
hydrophobicityColour.setLabel(MessageManager
- .getString("label.hydrophobicity"));
- hydrophobicityColour.addActionListener(this);
- helixColour
- .setLabel(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(this);
+ .getString("label.colourScheme_hydrophobic"));
+ hydrophobicityColour
+ .setName(JalviewColourScheme.Hydrophobic.toString());
+ hydrophobicityColour.addItemListener(this);
+ helixColour.setLabel(MessageManager
+ .getString("label.colourScheme_helix_propensity"));
+ helixColour.setName(JalviewColourScheme.Helix.toString());
+ helixColour.addItemListener(this);
strandColour.setLabel(MessageManager
- .getString("label.strand_propensity"));
- strandColour.addActionListener(this);
- turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(this);
- buriedColour.setLabel(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(this);
- abovePIDColour.setLabel(MessageManager
- .getString("label.above_identity_percentage"));
+ .getString("label.colourScheme_strand_propensity"));
+ strandColour.setName(JalviewColourScheme.Strand.toString());
+ strandColour.addItemListener(this);
+ turnColour.setLabel(MessageManager
+ .getString("label.colourScheme_turn_propensity"));
+ turnColour.setName(JalviewColourScheme.Turn.toString());
+ turnColour.addItemListener(this);
+ buriedColour.setLabel(MessageManager
+ .getString("label.colourScheme_buried_index"));
+ 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.percentage_identity"));
+
+ abovePIDColour.setLabel(MessageManager
+ .getString("label.above_identity_threshold"));
+ abovePIDColour.addItemListener(this);
+ modifyPID.setLabel(MessageManager
+ .getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(this);
+ conservationColour.setLabel(MessageManager
+ .getString("action.by_conservation"));
+ conservationColour.addItemListener(this);
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(this);
+
PIDColour.addActionListener(this);
- BLOSUM62Colour.setLabel("BLOSUM62");
BLOSUM62Colour.addActionListener(this);
- conservationMenuItem.setLabel(MessageManager
- .getString("label.conservation"));
editMenu.add(copy);
copy.addActionListener(this);
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
+ sg.cs = new ResidueShader(new ClustalxColourScheme(sg,
+ ap.av.getHiddenRepSequences()));
refresh();
}
protected void zappoColour_actionPerformed()
{
- getGroup().cs = new ZappoColourScheme();
+ getGroup().cs = new ResidueShader(new ZappoColourScheme());
refresh();
}
protected void taylorColour_actionPerformed()
{
- getGroup().cs = new TaylorColourScheme();
+ getGroup().cs = new ResidueShader(new TaylorColourScheme());
refresh();
}
protected void hydrophobicityColour_actionPerformed()
{
- getGroup().cs = new HydrophobicColourScheme();
+ getGroup().cs = new ResidueShader(new HydrophobicColourScheme());
refresh();
}
protected void helixColour_actionPerformed()
{
- getGroup().cs = new HelixColourScheme();
+ getGroup().cs = new ResidueShader(new HelixColourScheme());
refresh();
}
protected void strandColour_actionPerformed()
{
- getGroup().cs = new StrandColourScheme();
+ getGroup().cs = new ResidueShader(new StrandColourScheme());
refresh();
}
protected void turnColour_actionPerformed()
{
- getGroup().cs = new TurnColourScheme();
+ getGroup().cs = new ResidueShader(new TurnColourScheme());
refresh();
}
protected void buriedColour_actionPerformed()
{
- getGroup().cs = new BuriedColourScheme();
+ getGroup().cs = new ResidueShader(new BuriedColourScheme());
refresh();
}
public void nucleotideMenuItem_actionPerformed()
{
- getGroup().cs = new NucleotideColourScheme();
+ getGroup().cs = new ResidueShader(new NucleotideColourScheme());
+ refresh();
+ }
+
+ public void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(
+ new PurinePyrimidineColourScheme());
refresh();
}
else
// remove PIDColouring
{
+ SliderPanel.hidePIDSlider();
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
}
-
+ modifyPID.setEnabled(abovePIDColour.getState());
refresh();
-
}
protected void userDefinedColour_actionPerformed()
protected void PIDColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new PIDColourScheme();
+ sg.cs = new ResidueShader(new PIDColourScheme());
sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
.getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
{
SequenceGroup sg = getGroup();
- sg.cs = new Blosum62ColourScheme();
+ sg.cs = new ResidueShader(new Blosum62ColourScheme());
sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
.getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
return;
}
- if (conservationMenuItem.getState())
+ if (conservationColour.getState())
{
-
- sg.cs.setConservation(Conservation.calculateConservation("Group", 3,
- sg.getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
- .getAlignment().getWidth(), false, ap.av
- .getConsPercGaps(), false));
+ Conservation conservation = Conservation.calculateConservation(
+ "Group", sg
+ .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
+ .getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
+ false);
+ sg.getGroupColourScheme().setConservation(conservation);
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
else
// remove ConservationColouring
{
+ SliderPanel.hideConservationSlider();
sg.cs.setConservation(null);
}
-
+ modifyConservation.setEnabled(conservationColour.getState());
refresh();
}
git://source.jalview.org / jalview.git / blobdiff