/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
*/
-
package jalview.appletgui;
import java.util.*;
import jalview.util.UrlLink;
import jalview.io.AppletFormatAdapter;
-public class APopupMenu
- extends java.awt.PopupMenu implements ActionListener, ItemListener
+public class APopupMenu extends java.awt.PopupMenu implements
+ ActionListener, ItemListener
{
Menu groupMenu = new Menu();
+
MenuItem editGroupName = new MenuItem();
+
protected MenuItem clustalColour = new MenuItem();
+
protected MenuItem zappoColour = new MenuItem();
+
protected MenuItem taylorColour = new MenuItem();
+
protected MenuItem hydrophobicityColour = new MenuItem();
+
protected MenuItem helixColour = new MenuItem();
+
protected MenuItem strandColour = new MenuItem();
+
protected MenuItem turnColour = new MenuItem();
+
protected MenuItem buriedColour = new MenuItem();
+
protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
+
protected MenuItem userDefinedColour = new MenuItem();
+
protected MenuItem PIDColour = new MenuItem();
+
protected MenuItem BLOSUM62Colour = new MenuItem();
+
MenuItem noColourmenuItem = new MenuItem();
+
protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
final AlignmentPanel ap;
+
MenuItem unGroupMenuItem = new MenuItem();
+
MenuItem nucleotideMenuItem = new MenuItem();
+
Menu colourMenu = new Menu();
+
CheckboxMenuItem showBoxes = new CheckboxMenuItem();
+
CheckboxMenuItem showText = new CheckboxMenuItem();
+
CheckboxMenuItem showColourText = new CheckboxMenuItem();
+
Menu editMenu = new Menu("Edit");
+
MenuItem copy = new MenuItem("Copy (Jalview Only)");
+
MenuItem cut = new MenuItem("Cut (Jalview Only)");
+
MenuItem toUpper = new MenuItem("To Upper Case");
+
MenuItem toLower = new MenuItem("To Lower Case");
+
MenuItem toggleCase = new MenuItem("Toggle Case");
+
Menu outputmenu = new Menu();
+
Menu seqMenu = new Menu();
+
MenuItem pdb = new MenuItem();
+
MenuItem hideSeqs = new MenuItem();
+
MenuItem repGroup = new MenuItem();
+
MenuItem sequenceName = new MenuItem("Edit Name/Description");
+
MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
+
MenuItem editSequence = new MenuItem("Edit Sequence");
Sequence seq;
+
MenuItem revealAll = new MenuItem();
+
Menu menu1 = new Menu();
public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
{
- ///////////////////////////////////////////////////////////
+ // /////////////////////////////////////////////////////////
// If this is activated from the sequence panel, the user may want to
// edit or annotate a particular residue. Therefore display the residue menu
//
// If from the IDPanel, we must display the sequence menu
- //////////////////////////////////////////////////////////
+ // ////////////////////////////////////////////////////////
this.ap = apanel;
this.seq = seq;
try
{
jbInit();
- }
- catch (Exception e)
+ } catch (Exception e)
{
e.printStackTrace();
}
- for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;
- i++)
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
{
- MenuItem item = new MenuItem(jalview.io.AppletFormatAdapter.
- WRITEABLE_FORMATS[i]);
+ MenuItem item = new MenuItem(
+ jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
item.addActionListener(this);
outputmenu.add(item);
remove(groupMenu);
}
- if (links != null && links.size()>0)
+ if (links != null && links.size() > 0)
{
Menu linkMenu = new Menu("Link");
String link;
System.err.println(urlLink.getInvalidMessage());
continue;
}
- final String target = urlLink.getTarget(); // link.substring(0, link.indexOf("|"));
+ final String target = urlLink.getTarget(); // link.substring(0,
+ // link.indexOf("|"));
final String label = urlLink.getLabel();
if (urlLink.isDynamic())
{
// collect matching db-refs
- DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{target});
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
+ .getDBRef(), new String[]
+ { target });
// collect id string too
String id = seq.getName();
- if (dbr!=null)
+ if (dbr != null)
{
- for (int r=0;r<dbr.length; r++)
+ for (int r = 0; r < dbr.length; r++)
{
- if (id!=null && dbr[r].getAccessionId().equals(id))
+ if (id != null && dbr[r].getAccessionId().equals(id))
{
- // suppress duplicate link creation for the bare sequence ID string with this link
+ // 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)
+ String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
+ true);
+ if (urls != null)
{
- for (int u=0; u<urls.length; u+=2)
+ for (int u = 0; u < urls.length; u += 2)
{
- addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]);
+ addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
}
}
}
}
- if (id!=null)
+ if (id != null)
{
// create Bare ID link for this RUL
String[] urls = urlLink.makeUrls(id, true);
- if (urls!=null)
+ if (urls != null)
{
- for (int u=0; u<urls.length; u+=2)
+ for (int u = 0; u < urls.length; u += 2)
{
- addshowLink(linkMenu, label,urls[u+1]);
+ addshowLink(linkMenu, label, urls[u + 1]);
}
}
- // addshowLink(linkMenu, target, url_pref + id + url_suff);
+ // addshowLink(linkMenu, target, url_pref + id + url_suff);
}
- } else {
- addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
}
- /*final String url;
-
- if (link.indexOf("$SEQUENCE_ID$") > -1)
+ else
{
- // 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));
- } */
+ 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 (seq != null)
{
seqMenu.add(linkMenu);
remove(revealAll);
}
}
+
/**
* add a show URL menu item to the given linkMenu
+ *
* @param linkMenu
- * @param target - menu label string
- * @param url - url to open
+ * @param target -
+ * menu label string
+ * @param url -
+ * url to open
*/
- private void addshowLink(Menu linkMenu, final String target, final String url)
+ private void addshowLink(Menu linkMenu, final String target,
+ final String url)
{
addshowLink(linkMenu, target, target, url);
}
+
/**
* add a show URL menu item to the given linkMenu
+ *
* @param linkMenu
- * @param target - URL target window
- * @param label - menu label string
- * @param url - url to open
+ * @param target -
+ * URL target window
+ * @param label -
+ * menu label string
+ * @param url -
+ * url to open
*/
- private void addshowLink(Menu linkMenu, final String target, final String label, final String url)
+ private void addshowLink(Menu linkMenu, final String target,
+ final String label, final String url)
{
MenuItem item = new MenuItem(label);
item.addActionListener(new java.awt.event.ActionListener()
});
linkMenu.add(item);
}
-
public void itemStateChanged(ItemEvent evt)
{
else if (source == editGroupName)
{
- EditNameDialog dialog = new EditNameDialog(
- getGroup().getName(),
- getGroup().getDescription(),
- " Group Name",
- "Group Description",
- ap.alignFrame,
- "Edit Group Name / Description",
- 500,100, true);
+ EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
+ getGroup().getDescription(), " Group Name",
+ "Group Description", ap.alignFrame,
+ "Edit Group Name / Description", 500, 100, true);
if (dialog.accept)
{
{
ap.alignFrame.cut_actionPerformed();
}
- else if(source == editSequence)
+ else if (source == editSequence)
{
SequenceGroup sg = ap.av.getSelectionGroup();
- if(sg!=null)
+ if (sg != null)
{
if (seq == null)
seq = (Sequence) sg.getSequenceAt(0);
EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
- sg.getStartRes(),
- sg.getEndRes() + 1),
- null,
- "Edit Sequence ",
- null,
+ sg.getStartRes(), sg.getEndRes() + 1), null,
+ "Edit Sequence ", null,
- ap.alignFrame,
- "Edit Sequence",
- 500, 100, true);
+ ap.alignFrame, "Edit Sequence", 500, 100, true);
if (dialog.accept)
{
- EditCommand editCommand = new EditCommand(
- "Edit Sequences", EditCommand.REPLACE,
- dialog.getName().replace(' ', ap.av.getGapCharacter()),
- sg.getSequencesAsArray(ap.av.hiddenRepSequences),
- sg.getStartRes(), sg.getEndRes()+1, ap.av.alignment
- );
+ EditCommand editCommand = new EditCommand("Edit Sequences",
+ EditCommand.REPLACE, dialog.getName().replace(' ',
+ ap.av.getGapCharacter()), sg
+ .getSequencesAsArray(ap.av.hiddenRepSequences),
+ sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
}
}
}
regions.addElement(new int[]
- {start, end});
+ { start, end });
if (ap.av.hasHiddenColumns)
{
start = ap.av.colSel.adjustForHiddenColumns(end);
start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
}
- }
- while (end < sg.getEndRes());
+ } while (end < sg.getEndRes());
int[][] startEnd = new int[regions.size()][2];
for (int i = 0; i < regions.size(); i++)
caseChange = ChangeCaseCommand.TO_LOWER;
}
- ChangeCaseCommand caseCommand = new ChangeCaseCommand(
- description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
- startEnd, caseChange
- );
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+ sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
+ caseChange);
ap.alignFrame.addHistoryItem(caseCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
}
- else if(source == sequenceFeature)
+ else if (source == sequenceFeature)
{
SequenceGroup sg = ap.av.getSelectionGroup();
if (sg == null)
int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
int end = sg.findEndRes(sg.getSequenceAt(i));
features[i] = new SequenceFeature(null, null, null, start, end,
- "Jalview");
+ "Jalview");
}
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()
- .amendFeatures(seqs, features, true, ap))
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
{
ap.alignFrame.sequenceFeatures.setState(true);
ap.av.showSequenceFeatures(true);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- "Selection output - " + e.getActionCommand(),
- 600, 500);
+ jalview.bin.JalviewLite.addFrame(frame, "Selection output - "
+ + e.getActionCommand(), 600, 500);
- cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
- e.getActionCommand(),
- new Alignment(ap.av.getSelectionAsNewSequence()),
- ap.av.showJVSuffix));
+ cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(e
+ .getActionCommand(), new Alignment(ap.av
+ .getSelectionAsNewSequence()), ap.av.showJVSuffix));
}
void editName()
{
- EditNameDialog dialog = new EditNameDialog(
- seq.getName(),
- seq.getDescription(),
- " Sequence Name",
- "Sequence Description",
- ap.alignFrame,
- "Edit Sequence Name / Description",
- 500,100, true);
+ EditNameDialog dialog = new EditNameDialog(seq.getName(), seq
+ .getDescription(), " Sequence Name",
+ "Sequence Description", ap.alignFrame,
+ "Edit Sequence Name / Description", 500, 100, true);
if (dialog.accept)
{
void addPDB()
{
- if(seq.getPDBId()!=null)
+ if (seq.getPDBId() != null)
{
- PDBEntry entry = (PDBEntry)seq.getPDBId().firstElement();
+ PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
- if ( ap.av.applet.jmolAvailable )
- new jalview.appletgui.AppletJmol(entry,
- new Sequence[]{seq},
- null,
- ap,
- AppletFormatAdapter.URL);
- else
- new MCview.AppletPDBViewer(entry,
- new Sequence[]{seq},
- null,
- ap,
- AppletFormatAdapter.URL);
+ if (ap.av.applet.jmolAvailable)
+ new jalview.appletgui.AppletJmol(entry, new Sequence[]
+ { seq }, null, ap, AppletFormatAdapter.URL);
+ else
+ new MCview.AppletPDBViewer(entry, new Sequence[]
+ { seq }, null, ap, AppletFormatAdapter.URL);
}
else
}
}
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
groupMenu.setLabel("Group");
groupMenu.setLabel("Selection");
protected void clustalColour_actionPerformed()
{
SequenceGroup sg = getGroup();
- sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
- ap.av.alignment.getWidth());
+ sg.cs = new ClustalxColourScheme(sg
+ .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
+ .getWidth());
refresh();
}
if (abovePIDColour.getState())
{
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
- hiddenRepSequences), 0,
- ap.av.alignment.getWidth()));
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
- getGroup().getName());
+ sg.cs.setConsensus(AAFrequency.calculate(sg
+ .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
+ .getWidth()));
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ .getName());
sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
SliderPanel.showPIDSlider();
}
- else // remove PIDColouring
+ else
+ // remove PIDColouring
{
sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
}
{
SequenceGroup sg = getGroup();
sg.cs = new PIDColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
- hiddenRepSequences), 0,
- ap.av.alignment.getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(sg
+ .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
+ .getWidth()));
refresh();
}
sg.cs = new Blosum62ColourScheme();
- sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
- hiddenRepSequences), 0,
- ap.av.alignment.getWidth()));
+ sg.cs.setConsensus(AAFrequency.calculate(sg
+ .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
+ .getWidth()));
refresh();
}
{
Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(ap.av.
- hiddenRepSequences), 0,
- ap.av.alignment.getWidth());
+ ResidueProperties.propHash, 3, sg
+ .getSequences(ap.av.hiddenRepSequences), 0,
+ ap.av.alignment.getWidth());
c.calculate();
c.verdict(false, ap.av.ConsPercGaps);
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
- else // remove ConservationColouring
+ else
+ // remove ConservationColouring
{
sg.cs.setConservation(null);
}
if (sg == null || sg.getSize() < 1)
{
ap.av.hideSequence(new SequenceI[]
- {seq});
+ { seq });
return;
}
git://source.jalview.org / jalview.git / blobdiff