/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.appletgui;
import java.util.*;
import jalview.commands.*;
import jalview.datamodel.*;
import jalview.schemes.*;
+import jalview.util.MessageManager;
+import jalview.util.UrlLink;
import jalview.io.AppletFormatAdapter;
+import jalview.io.SequenceAnnotationReport;
-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 createGroupMenuItem = 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");
+
+ CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
+
+ Menu editMenu = new Menu(MessageManager.getString("action.edit"));
+
+ MenuItem copy = new MenuItem(MessageManager.getString("label.jalview_copy"));
+
+ MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
+
+ MenuItem toUpper = new MenuItem(MessageManager.getString("label.to_upper_case"));
+
+ MenuItem toLower = new MenuItem(MessageManager.getString("label.to_lower_case"));
+
+ MenuItem toggleCase = new MenuItem(MessageManager.getString("label.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");
+
+ MenuItem sequenceName = new MenuItem(MessageManager.getString("label.edit_name_description"));
+
+ MenuItem sequenceFeature = new MenuItem(MessageManager.getString("label.create_sequence_feature"));
+
+ MenuItem editSequence = new MenuItem(MessageManager.getString("label.edit_sequence"));
+
+ MenuItem sequenceDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
+
+ MenuItem selSeqDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
Sequence seq;
+
MenuItem revealAll = new MenuItem();
+
+ MenuItem revealSeq = new MenuItem();
+
+ /**
+ * index of sequence to be revealed
+ */
+ int revealSeq_index = -1;
+
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);
if (sg != null && sg.getSize() > 0)
{
- editGroupName.setLabel(sg.getName());
+ editGroupName.setLabel(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
showText.setState(sg.getDisplayText());
showColourText.setState(sg.getColourText());
showBoxes.setState(sg.getDisplayBoxes());
- if (!ap.av.alignment.getGroups().contains(sg))
+ displayNonconserved.setState(sg.getShowNonconserved());
+ if (!ap.av.getAlignment().getGroups().contains(sg))
{
+ menu1.setLabel(MessageManager.getString("action.edit_new_group"));
groupMenu.remove(unGroupMenuItem);
+ } else {
+ menu1.setLabel(MessageManager.getString("action.edit_group"));
+ groupMenu.remove(createGroupMenuItem);
}
}
remove(groupMenu);
}
- if (links != null && links.size()>0)
+ if (links != null && links.size() > 0)
{
- Menu linkMenu = new Menu("Link");
+ Menu linkMenu = new Menu(MessageManager.getString("action.link"));
String link;
for (int i = 0; i < links.size(); i++)
{
link = links.elementAt(i).toString();
- final String target = link.substring(0, link.indexOf("|"));
-
- final String url;
-
- if (link.indexOf("$SEQUENCE_ID$") > -1)
+ 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())
{
- // 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});
+ DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
+ seq.getDBRef(), new String[]
+ { target });
// collect id string too
String id = seq.getName();
- if (id.indexOf("|") > -1)
+ String descr = seq.getDescription();
+ if (descr != null && descr.length() < 1)
{
- id = id.substring(id.lastIndexOf("|") + 1);
+ descr = null;
}
- if (dbr!=null)
+ if (dbr != null)
{
- for (int r=0;r<dbr.length; r++)
+ for (int r = 0; r < dbr.length; r++)
{
- if (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;
}
- addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
- url_pref+dbr[r].getAccessionId()+url_suff);
+ // 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)
+ if (id != null)
{
// create Bare ID link for this RUL
- addshowLink(linkMenu, target, url_pref + id + url_suff);
+ 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, link.substring(link.lastIndexOf("|")+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 (seq != null)
+ if (linkMenu.getItemCount() > 0)
{
- seqMenu.add(linkMenu);
- }
- else
- {
- add(linkMenu);
+ if (seq != null)
+ {
+ seqMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
}
}
+ // TODO: add group link menu entry here
if (seq != null)
{
seqMenu.setLabel(seq.getName());
- repGroup.setLabel("Represent Group with " + seq.getName());
+ repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
}
else
{
remove(seqMenu);
}
- if (!ap.av.hasHiddenRows)
+ if (!ap.av.hasHiddenRows())
{
remove(revealAll);
+ remove(revealSeq);
+ }
+ else
+ {
+ final int index = ap.av.getAlignment().findIndex(seq);
+
+ if (ap.av.adjustForHiddenSeqs(index)
+ - ap.av.adjustForHiddenSeqs(index - 1) > 1)
+ {
+ revealSeq_index = index;
+ }
+ else
+ {
+ remove(revealSeq);
+ }
}
}
+
/**
* 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)
{
{
showBoxes_itemStateChanged();
}
+ else if (evt.getSource() == displayNonconserved)
+ {
+ this.showNonconserved_itemStateChanged();
+ }
}
public void actionPerformed(ActionEvent evt)
unGroupMenuItem_actionPerformed();
}
+ else if (source == createGroupMenuItem)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+
else if (source == sequenceName)
{
editName();
}
+ else if (source == sequenceDetails)
+ {
+ showSequenceDetails();
+ }
+ else if (source == selSeqDetails)
+ {
+ showSequenceSelectionDetails();
+ }
else if (source == pdb)
{
addPDB();
{
hideSequences(true);
}
+ else if (source == revealSeq)
+ {
+ ap.av.showSequence(revealSeq_index);
+ }
else if (source == revealAll)
{
ap.av.showAllHiddenSeqs();
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.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1,
+ ap.av.getAlignment());
ap.alignFrame.addHistoryItem(editCommand);
- ap.av.firePropertyChange("alignment", null,
- ap.av.getAlignment().getSequences());
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
+ .getSequences());
}
}
}
Vector regions = new Vector();
if (sg != null)
{
- int start = sg.getStartRes();
- int end = sg.getEndRes() + 1;
-
- do
- {
- if (ap.av.hasHiddenColumns)
- {
- if (start == 0)
- {
- start = ap.av.colSel.adjustForHiddenColumns(start);
- }
-
- end = ap.av.colSel.getHiddenBoundaryRight(start);
- if (start == end)
- {
- end = sg.getEndRes() + 1;
- }
- if (end > sg.getEndRes())
- {
- end = sg.getEndRes() + 1;
- }
- }
-
- regions.addElement(new int[]
- {start, end});
-
- if (ap.av.hasHiddenColumns)
- {
- start = ap.av.colSel.adjustForHiddenColumns(end);
- start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
- }
- }
- while (end < sg.getEndRes());
-
- int[][] startEnd = new int[regions.size()][2];
- for (int i = 0; i < regions.size(); i++)
- {
- startEnd[i] = (int[]) regions.elementAt(i);
- }
+ int[][] startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
String description;
int caseChange;
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.getHiddenRepSequences()),
+ 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)
return;
}
- int gSize = sg.getSize();
- SequenceI[] seqs = new SequenceI[gSize];
- SequenceFeature[] features = new SequenceFeature[gSize];
+ int rsize = 0, gSize = sg.getSize();
+ SequenceI[] rseqs, seqs = new SequenceI[gSize];
+ SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
for (int i = 0; i < gSize; i++)
{
- seqs[i] = sg.getSequenceAt(i);
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");
+ if (start <= end)
+ {
+ seqs[rsize] = sg.getSequenceAt(i);
+ features[rsize] = new SequenceFeature(null, null, null, start,
+ end, "Jalview");
+ rsize++;
+ }
}
-
- if (ap.seqPanel.seqCanvas.getFeatureRenderer()
- .amendFeatures(seqs, features, true, ap))
+ rseqs = new SequenceI[rsize];
+ tfeatures = new SequenceFeature[rsize];
+ System.arraycopy(seqs, 0, rseqs, 0, rsize);
+ System.arraycopy(features, 0, tfeatures, 0, rsize);
+ features = tfeatures;
+ seqs = rseqs;
+
+ 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);
+ MessageManager.formatMessage("label.selection_output_command", new String[]{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(),
- new Alignment(ap.av.getSelectionAsNewSequence()),
- ap.av.showJVSuffix));
+ e.getActionCommand(),
+ new Alignment(ap.av.getSelectionAsNewSequence()),
+ ap.av.showJVSuffix));
+
+ }
+ protected void showSequenceSelectionDetails()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void showSequenceDetails()
+ {
+ createSequenceDetailsReport(new SequenceI[]
+ { seq });
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+
+ StringBuffer contents = new StringBuffer();
+ for (SequenceI seq : sequences)
+ {
+ contents.append(MessageManager.formatMessage("label.annotation_for_displayid",new String[]{seq.getDisplayId(true)}));
+ new SequenceAnnotationReport(null)
+ .createSequenceAnnotationReport(
+ contents,
+ seq,
+ true,
+ true,
+ false,
+ (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
+ : null);
+ contents.append("</p>");
+ }
+ Frame frame = new Frame();
+ frame.add(cap);
+ jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
+ + (sequences.length == 1 ? sequences[0].getDisplayId(true)
+ : "Selection"), 600, 500);
+ cap.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
}
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
{
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
- cap.setText("Paste your PDB file here.");
+ cap.setText(MessageManager.getString("label.paste_pdb_file"));
cap.setPDBImport(seq);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.formatMessage("label.paste_pdb_file_for_sequence", new String[]{seq.getName()}), 400, 300);
}
}
- private void jbInit()
- throws Exception
+ private void jbInit() throws Exception
{
- groupMenu.setLabel("Group");
- groupMenu.setLabel("Selection");
+ groupMenu.setLabel(MessageManager.getString("label.selection"));
sequenceFeature.addActionListener(this);
editGroupName.addActionListener(this);
- unGroupMenuItem.setLabel("Remove Group");
+ unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group"));
unGroupMenuItem.addActionListener(this);
- nucleotideMenuItem.setLabel("Nucleotide");
+ createGroupMenuItem.setLabel(MessageManager.getString("action.create_group"));
+ createGroupMenuItem.addActionListener(this);
+
+ nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide"));
nucleotideMenuItem.addActionListener(this);
conservationMenuItem.addItemListener(this);
abovePIDColour.addItemListener(this);
- colourMenu.setLabel("Group Colour");
- showBoxes.setLabel("Boxes");
+ colourMenu.setLabel(MessageManager.getString("label.group_colour"));
+ showBoxes.setLabel(MessageManager.getString("action.boxes"));
showBoxes.setState(true);
showBoxes.addItemListener(this);
sequenceName.addActionListener(this);
-
- showText.setLabel("Text");
+ sequenceDetails.addActionListener(this);
+ selSeqDetails.addActionListener(this);
+ displayNonconserved.setLabel(MessageManager.getString("label.show_non_conversed"));
+ displayNonconserved.setState(false);
+ displayNonconserved.addItemListener(this);
+ showText.setLabel(MessageManager.getString("action.text"));
showText.addItemListener(this);
- showColourText.setLabel("Colour Text");
+ showColourText.setLabel(MessageManager.getString("label.colour_text"));
showColourText.addItemListener(this);
- outputmenu.setLabel("Output to Textbox...");
- seqMenu.setLabel("Sequence");
- pdb.setLabel("View PDB Structure");
- hideSeqs.setLabel("Hide Sequences");
- repGroup.setLabel("Represent Group with");
- revealAll.setLabel("Reveal All");
- menu1.setLabel("Group");
+ outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+ seqMenu.setLabel(MessageManager.getString("label.sequence"));
+ pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
+ hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
+ repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{""}));
+ revealAll.setLabel(MessageManager.getString("action.reveal_all"));
+ revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
+ menu1.setLabel(MessageManager.getString("label.group")+":");
add(groupMenu);
this.add(seqMenu);
this.add(hideSeqs);
+ this.add(revealSeq);
this.add(revealAll);
- groupMenu.add(editGroupName);
+ // groupMenu.add(selSeqDetails);
groupMenu.add(editMenu);
groupMenu.add(outputmenu);
groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
groupMenu.add(menu1);
colourMenu.add(noColourmenuItem);
toLower.addActionListener(this);
editMenu.add(toggleCase);
seqMenu.add(sequenceName);
- seqMenu.add(pdb);
+ // seqMenu.add(sequenceDetails);
+
+ if (!ap.av.applet.useXtrnalSviewer)
+ {
+ seqMenu.add(pdb);
+ }
seqMenu.add(repGroup);
- menu1.add(unGroupMenuItem);
+ menu1.add(editGroupName);
menu1.add(colourMenu);
menu1.add(showBoxes);
menu1.add(showText);
menu1.add(showColourText);
+ menu1.add(displayNonconserved);
toggleCase.addActionListener(this);
pdb.addActionListener(this);
hideSeqs.addActionListener(this);
repGroup.addActionListener(this);
revealAll.addActionListener(this);
+ revealSeq.addActionListener(this);
}
void refresh()
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, ap.av.getHiddenRepSequences());
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
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().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
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().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
+ .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
refresh();
}
if (conservationMenuItem.getState())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3,
- sg.getSequences(ap.av.
- hiddenRepSequences), 0,
- ap.av.alignment.getWidth());
-
- c.calculate();
- c.verdict(false, ap.av.ConsPercGaps);
-
- sg.cs.setConservation(c);
-
+ sg.cs.setConservation(Conservation.calculateConservation("Group",
+ ResidueProperties.propHash, 3, sg.getSequences(ap.av
+ .getHiddenRepSequences()), 0, ap.av.getAlignment()
+ .getWidth(), false, ap.av.getConsPercGaps(), false));
SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
SliderPanel.showConservationSlider();
}
- else // remove ConservationColouring
+ else
+ // remove ConservationColouring
{
sg.cs.setConservation(null);
}
// this method won't add a new group if it already exists
if (sg != null)
{
- ap.av.alignment.addGroup(sg);
+ ap.av.getAlignment().addGroup(sg);
}
return sg;
void unGroupMenuItem_actionPerformed()
{
SequenceGroup sg = ap.av.getSelectionGroup();
- ap.av.alignment.deleteGroup(sg);
+ ap.av.getAlignment().deleteGroup(sg);
ap.av.setSelectionGroup(null);
ap.paintAlignment(true);
}
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly create group
+ refresh();
+ }
+
public void showColourText_itemStateChanged()
{
getGroup().setColourText(showColourText.getState());
refresh();
}
+ public void showNonconserved_itemStateChanged()
+ {
+ getGroup().setShowNonconserved(this.displayNonconserved.getState());
+ refresh();
+ }
+
public void showBoxes_itemStateChanged()
{
getGroup().setDisplayBoxes(showBoxes.getState());
if (sg == null || sg.getSize() < 1)
{
ap.av.hideSequence(new SequenceI[]
- {seq});
+ { seq });
return;
}
}
ap.av.hideSequence(hseqs);
+ ap.av.sendSelection();
}
}
git://source.jalview.org / jalview.git / blobdiff