/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
import jalview.io.SequenceAnnotationReport;
import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.TurnColourScheme;
import jalview.schemes.UserColourScheme;
import jalview.schemes.ZappoColourScheme;
-import jalview.util.DBRefUtils;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
import java.awt.Color;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
-import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.Hashtable;
import java.util.LinkedHashMap;
import javax.swing.JColorChooser;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPopupMenu;
import javax.swing.JRadioButtonMenuItem;
protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
- protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
-
protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
+ protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
+
+ protected JMenuItem modifyPID = new JMenuItem();
+
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
+ protected JMenuItem modifyConservation = new JMenuItem();
+
AlignmentPanel ap;
JMenu sequenceMenu = new JMenu();
colours.add(strandColour);
colours.add(turnColour);
colours.add(buriedColour);
- colours.add(abovePIDColour);
colours.add(userDefinedColour);
colours.add(PIDColour);
colours.add(BLOSUM62Colour);
colours.add(purinePyrimidineColour);
colours.add(RNAInteractionColour);
- for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
+ for (String ff : FileFormats.getInstance().getWritableFormats(true))
{
- JMenuItem item = new JMenuItem(
- jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
+ JMenuItem item = new JMenuItem(ff);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
menuItem.setText(MessageManager.formatMessage(
"label.2d_rna_structure_line",
new Object[] { aa.label }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
menuItem.setText(MessageManager.formatMessage(
"label.2d_rna_sequence_name",
new Object[] { seq.getName() }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
menuItem = new JMenuItem(
MessageManager.getString("action.hide_sequences"));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
menuItem = new JMenuItem(MessageManager.formatMessage(
"label.represent_group_with",
new Object[] { seq.getName() }));
- menuItem.addActionListener(new java.awt.event.ActionListener()
+ menuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
noColourmenuItem.setSelected(true);
}
- if (sg.cs != null && sg.cs.conservationApplied())
+ if (sg.cs != null)
{
- conservationMenuItem.setSelected(true);
+ if (sg.cs.conservationApplied())
+ {
+ conservationMenuItem.setSelected(true);
+ }
+ if (sg.cs.getThreshold() > 0)
+ {
+ abovePIDColour.setSelected(true);
+ }
}
+ modifyConservation.setEnabled(conservationMenuItem.isSelected());
+ modifyPID.setEnabled(abovePIDColour.isSelected());
displayNonconserved.setSelected(sg.getShowNonconserved());
showText.setSelected(sg.getDisplayText());
showColourText.setSelected(sg.getColourText());
void addFeatureLinks(final SequenceI seq, List<String> links)
{
JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
- List<String> linkset = new ArrayList<String>();
+ Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
+
for (String link : links)
{
UrlLink urlLink = null;
Cache.log.error("Exception for URLLink '" + link + "'", foo);
continue;
}
- ;
+
if (!urlLink.isValid())
{
Cache.log.error(urlLink.getInvalidMessage());
continue;
}
- final String label = urlLink.getLabel();
- if (seq != null && urlLink.isDynamic())
- {
- // collect matching db-refs
- DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] { urlLink.getTarget() });
- // collect id string too
- String id = seq.getName();
- String descr = seq.getDescription();
- if (descr != null && descr.length() < 1)
- {
- descr = null;
- }
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
- 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 URL
- String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.add(urls[u] + "|" + urls[u + 1]);
- addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
- }
- }
- }
- }
- }
- if (id != null)
- {
- // create Bare ID link for this URL
- String[] urls = urlLink.makeUrls(id, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.add(urls[u] + "|" + urls[u + 1]);
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- // Create urls from description but only for URL links which are regex
- // links
- if (descr != null && urlLink.getRegexReplace() != null)
- {
- // create link for this URL from description where regex matches
- String[] urls = urlLink.makeUrls(descr, true);
- if (urls != null)
- {
- for (int u = 0; u < urls.length; u += 2)
- {
- if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
- {
- linkset.add(urls[u] + "|" + urls[u + 1]);
- addshowLink(linkMenu, label, urls[u + 1]);
- }
- }
- }
- }
- }
- else
- {
- if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
- {
- linkset.add(label + "|" + urlLink.getUrl_prefix());
- // Add a non-dynamic link
- addshowLink(linkMenu, label, urlLink.getUrl_prefix());
- }
- }
+ 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 (sequence != null)
{
sequenceMenu.add(linkMenu);
{
add(linkMenu);
}
+
}
/**
label = label.substring(1, label.length() - 1); // a, b, c
final JMenuItem item = new JMenuItem(label);
item.setToolTipText(calcId);
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
}
+ private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
+ {
+ for (List<String> linkstrset : linkset)
+ {
+ // split linkstr into label and url
+ addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
+ }
+ }
+
/**
* add a show URL menu item to the given linkMenu
*
JMenuItem item = new JMenuItem(label);
item.setToolTipText(MessageManager.formatMessage(
"label.open_url_param", new Object[] { url }));
- item.addActionListener(new java.awt.event.ActionListener()
+ item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
groupMenu.setText(MessageManager.getString("label.selection"));
groupName.setText(MessageManager.getString("label.name"));
- groupName.addActionListener(new java.awt.event.ActionListener()
+ groupName.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
sequenceMenu.setText(MessageManager.getString("label.sequence"));
sequenceName.setText(MessageManager
.getString("label.edit_name_description"));
- sequenceName.addActionListener(new java.awt.event.ActionListener()
+ sequenceName.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
chooseAnnotations.setText(MessageManager
.getString("action.choose_annotations"));
- chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
+ chooseAnnotations.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
sequenceDetails.setText(MessageManager
.getString("label.sequence_details"));
- sequenceDetails.addActionListener(new java.awt.event.ActionListener()
+ sequenceDetails.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
sequenceSelDetails.setText(MessageManager
.getString("label.sequence_details"));
- sequenceSelDetails
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- sequenceSelectionDetails_actionPerformed();
- }
- });
+ sequenceSelDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }
+ });
PIDColour.setFocusPainted(false);
unGroupMenuItem
.setText(MessageManager.getString("action.remove_group"));
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
+ unGroupMenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
createGroupMenuItem.setText(MessageManager
.getString("action.create_group"));
- createGroupMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- createGroupMenuItem_actionPerformed();
- }
- });
+ createGroupMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
outline.setText(MessageManager.getString("action.border_colour"));
- outline.addActionListener(new java.awt.event.ActionListener()
+ outline.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
colourMenu.addSeparator();
colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
editMenu.add(copy);
editMenu.add(cut);
editMenu.add(editSequence);
jMenu1.add(outline);
jMenu1.add(displayNonconserved);
noColourmenuItem.setText(MessageManager.getString("label.none"));
- noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
+ noColourmenuItem.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
clustalColour.setText(MessageManager
.getString("label.clustalx_colours"));
- clustalColour.addActionListener(new java.awt.event.ActionListener()
+ clustalColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
zappoColour.setText(MessageManager.getString("label.zappo"));
- zappoColour.addActionListener(new java.awt.event.ActionListener()
+ zappoColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
taylorColour.setText(MessageManager.getString("label.taylor"));
- taylorColour.addActionListener(new java.awt.event.ActionListener()
+ taylorColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
hydrophobicityColour.setText(MessageManager
.getString("label.hydrophobicity"));
- hydrophobicityColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- hydrophobicityColour_actionPerformed();
- }
- });
+ hydrophobicityColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hydrophobicityColour_actionPerformed();
+ }
+ });
helixColour.setText(MessageManager.getString("label.helix_propensity"));
- helixColour.addActionListener(new java.awt.event.ActionListener()
+ helixColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
strandColour.setText(MessageManager
.getString("label.strand_propensity"));
- strandColour.addActionListener(new java.awt.event.ActionListener()
+ strandColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
turnColour.setText(MessageManager.getString("label.turn_propensity"));
- turnColour.addActionListener(new java.awt.event.ActionListener()
+ turnColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
buriedColour.setText(MessageManager.getString("label.buried_index"));
- buriedColour.addActionListener(new java.awt.event.ActionListener()
+ buriedColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
buriedColour_actionPerformed();
}
});
- abovePIDColour.setText(MessageManager
- .getString("label.above_identity_percentage"));
- abovePIDColour.addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- abovePIDColour_actionPerformed();
- }
- });
userDefinedColour.setText(MessageManager
.getString("action.user_defined"));
- userDefinedColour.addActionListener(new java.awt.event.ActionListener()
+ userDefinedColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
PIDColour
.setText(MessageManager.getString("label.percentage_identity"));
- PIDColour.addActionListener(new java.awt.event.ActionListener()
+ PIDColour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
}
});
BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
- BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
+ BLOSUM62Colour.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
});
purinePyrimidineColour.setText(MessageManager
.getString("label.purine_pyrimidine"));
- purinePyrimidineColour
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- purinePyrimidineColour_actionPerformed();
- }
- });
+ purinePyrimidineColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ purinePyrimidineColour_actionPerformed();
+ }
+ });
/*
- * covariationColour.addActionListener(new java.awt.event.ActionListener() {
+ * covariationColour.addActionListener(new ActionListener() {
* public void actionPerformed(ActionEvent e) {
* covariationColour_actionPerformed(); } });
*/
+ abovePIDColour.setText(MessageManager
+ .getString("label.above_identity_percentage"));
+ abovePIDColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDColour_actionPerformed();
+ }
+ });
+
+ modifyPID.setText(MessageManager
+ .getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
conservationMenuItem.setText(MessageManager
.getString("label.conservation"));
- conservationMenuItem
- .addActionListener(new java.awt.event.ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent e)
- {
- conservationMenuItem_actionPerformed();
- }
- });
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ });
+
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
+ }
+ });
+ }
+
+ protected void modifyConservation_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ protected void modifyPID_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ // .getName());
+ // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ .getName());
+ SliderPanel.showPIDSlider();
+ }
}
/**
public void createSequenceDetailsReport(SequenceI[] sequences)
{
CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
- StringBuffer contents = new StringBuffer();
+ StringBuilder contents = new StringBuilder(128);
for (SequenceI seq : sequences)
{
contents.append("<p><h2>"
seq,
true,
true,
- false,
(ap.getSeqPanel().seqCanvas.fr != null) ? ap
.getSeqPanel().seqCanvas.fr.getMinMax()
: null);
return;
}
- if (abovePIDColour.isSelected())
+ boolean selected = abovePIDColour.isSelected();
+ if (selected)
{
sg.cs.setConsensus(AAFrequency.calculate(
sg.getSequences(ap.av.getHiddenRepSequences()),
// remove PIDColouring
{
sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.hidePIDSlider();
}
+ modifyPID.setEnabled(selected);
refresh();
}
return;
}
- if (conservationMenuItem.isSelected())
+ boolean selected = conservationMenuItem.isSelected();
+ if (selected)
{
// JBPNote: Conservation name shouldn't be i18n translated
- Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av
+ Conservation c = new Conservation("Group", sg.getSequences(ap.av
.getHiddenRepSequences()), sg.getStartRes(),
sg.getEndRes() + 1);
// remove ConservationColouring
{
sg.cs.setConservation(null);
+ SliderPanel.hideConservationSlider();
}
+ modifyConservation.setEnabled(selected);
refresh();
}
{
if (dialog.getName().indexOf(" ") > -1)
{
- JOptionPane
+ JvOptionPane
.showMessageDialog(
ap,
MessageManager
.getString("label.spaces_converted_to_backslashes"),
MessageManager
.getString("label.no_spaces_allowed_sequence_name"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
}
sequence.setName(dialog.getName().replace(' ', '_'));
jalview.util.BrowserLauncher.openURL(url);
} catch (Exception ex)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.web_browser_not_found_unix"),
MessageManager.getString("label.web_browser_not_found"),
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.WARNING_MESSAGE);
ex.printStackTrace();
}
// or we simply trust the user wants
// wysiwig behaviour
- cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
- ap, true));
+ FileFormatI fileFormat = FileFormats.getInstance().forName(
+ e.getActionCommand());
+ cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
}
public void sequenceFeature_actionPerformed()