+ You can copy the currently highlighted matching regions of sequences to the clipboard with alt-Command-C.
+
+
Control 'V' |
Both |
Paste the contents of the clipboard to the current
diff --git a/help/help/html/menus/alignmentMenu.html b/help/help/html/menus/alignmentMenu.html
index 6532933..1a7286f 100755
--- a/help/help/html/menus/alignmentMenu.html
+++ b/help/help/html/menus/alignmentMenu.html
@@ -169,6 +169,16 @@
paste the clipboard contents to a text editor, you will see
the format of the copied residues FASTA.
+ Copy Highlighted region (Control Shift
+ C) Copies each stretch of highlighted
+ residues as a new sequence on the system clipboard - you can
+ also do this by pressing <CTRL> <SHIFT> and C
+ (<APPLE> <SHIFT> and C on MacOSX). Use
+ this when you want to extract sequence regions highlighted
+ as a result of a Find operation, or due to mouseovers or
+ selections made in other views such as an assocated 3D
+ structure viewer.
+
Paste
- To New Alignment (Control Shift V)
diff --git a/help/help/html/menus/alwedit.html b/help/help/html/menus/alwedit.html
index eb8e839..7384cda 100755
--- a/help/help/html/menus/alwedit.html
+++ b/help/help/html/menus/alwedit.html
@@ -49,6 +49,15 @@
and C on MacOSX). If you try to paste the clipboard
contents to a text editor, you will see the format of the copied
residues FASTA.
+
+ - Copy Highlighted region (Control Shift C)
Copies
+ each stretch of highlighted residues as a new sequence on the
+ system clipboard - you can also do this by pressing <CTRL>
+ <SHIFT> and C (<APPLE> <SHIFT> and C on
+ MacOSX). Use this when you want to extract sequence regions
+ highlighted as a result of a Find operation, or due to
+ mouseovers or selections made in other views such as an
+ assocated 3D structure viewer.
- Paste
diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 3843ddb..30a154d 100644
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -130,6 +130,8 @@ action.calculate = Calculate
action.select_all = Select all
action.select_highlighted_columns = Select Highlighted Columns
tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-(or Cmd)-B to toggle, and Alt-B to mark all but highlighted columns
+action.copy_highlighted_regions = Copy Highlighted Regions
+tooltip.copy_highlighted_regions = Copies highlighted sequence regions to the clipboard for export or further analysis
action.deselect_all = Deselect all
action.invert_selection = Invert selection
action.using_jmol = Using Jmol
@@ -1398,6 +1400,8 @@ label.click_to_edit = Click to edit, right-click for menu
label.by_annotation_tooltip = Annotation Colour is configured from the main Colour menu
label.show_linked_features = Show {0} features
label.on_top = on top
+label.include_features = Include Features
+label.search_features = Search descriptions of displayed features
label.include_linked_features = Include {0} features
label.include_linked_tooltip = Include visible {0} features converted to local sequence coordinates
label.features_not_shown = {0} feature(s) not shown
@@ -1406,6 +1410,7 @@ label.ignore_hidden = Ignore hidden columns
label.ignore_hidden_tooltip = Ignore any characters in hidden columns when matching
label.log_level = Log level
label.log_level_tooltip = Temporarily set the log level for this console. The log level will revert to {0} when this Java console is closed.
+label.copy = Copy
label.copy_to_clipboard = Copy to clipboard
label.copy_to_clipboard_tooltip = Copy all of the log text in this console to the system clipboard
label.startup = Startup
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index f8cfcbf..21fa2f1 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -20,26 +20,28 @@
*/
package jalview.analysis;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
import java.util.Locale;
+import com.stevesoft.pat.Regex;
+
import jalview.api.AlignViewportI;
+import jalview.api.FeatureRenderer;
import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
import jalview.util.Comparison;
import jalview.util.MapList;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.List;
-
-import com.stevesoft.pat.Regex;
-
/**
* Implements the search algorithm for the Find dialog
*/
@@ -61,6 +63,11 @@ public class Finder implements FinderI
private AlignViewportI viewport;
/*
+ * feature renderer model - if available
+ */
+ FeatureRenderer frm = null;
+
+ /*
* sequence index in alignment to search from
*/
private int sequenceIndex;
@@ -72,6 +79,16 @@ public class Finder implements FinderI
private int residueIndex;
/*
+ * last feature matched when incrementally searching sequence features
+ */
+ private SequenceFeature lastFeature;
+
+ /*
+ * last sequenceIndex used when lastFeature was discovered
+ */
+ private int lastFeatureSequenceIndex;
+
+ /*
* the true sequence position of the start of the
* last sequence searched (when 'ignore hidden regions' does not apply)
*/
@@ -99,30 +116,36 @@ public class Finder implements FinderI
@Override
public void findAll(String theSearchString, boolean matchCase,
- boolean searchDescription, boolean ignoreHidden)
+ boolean searchDescription, boolean searchFeatureDesc,
+ boolean ignoreHidden)
{
/*
* search from the start
*/
+ lastFeature = null;
+ lastFeatureSequenceIndex = 0;
sequenceIndex = 0;
residueIndex = -1;
- doFind(theSearchString, matchCase, searchDescription, true,
- ignoreHidden);
+ doFind(theSearchString, matchCase, searchDescription, searchFeatureDesc,
+ true, ignoreHidden);
/*
* reset to start for next search
*/
sequenceIndex = 0;
residueIndex = -1;
+ lastFeature = null;
+ lastFeatureSequenceIndex = 0;
}
@Override
public void findNext(String theSearchString, boolean matchCase,
- boolean searchDescription, boolean ignoreHidden)
+ boolean searchDescription, boolean searchFeatureDesc,
+ boolean ignoreHidden)
{
- doFind(theSearchString, matchCase, searchDescription, false,
- ignoreHidden);
+ doFind(theSearchString, matchCase, searchDescription, searchFeatureDesc,
+ false, ignoreHidden);
if (searchResults.isEmpty() && idMatches.isEmpty())
{
@@ -131,6 +154,8 @@ public class Finder implements FinderI
*/
sequenceIndex = 0;
residueIndex = -1;
+ lastFeature = null;
+ lastFeatureSequenceIndex = 0;
}
}
@@ -144,7 +169,8 @@ public class Finder implements FinderI
* @param ignoreHidden
*/
protected void doFind(String theSearchString, boolean matchCase,
- boolean searchDescription, boolean findAll, boolean ignoreHidden)
+ boolean searchDescription, boolean searchFeatureDesc,
+ boolean findAll, boolean ignoreHidden)
{
searchResults = new SearchResults();
idMatches = new ArrayList<>();
@@ -169,7 +195,7 @@ public class Finder implements FinderI
while ((!found || findAll) && sequenceIndex < end)
{
found = findNextMatch(searchString, searchPattern, searchDescription,
- ignoreHidden);
+ searchFeatureDesc, ignoreHidden);
}
}
@@ -350,7 +376,8 @@ public class Finder implements FinderI
* @return
*/
protected boolean findNextMatch(String searchString, Regex searchPattern,
- boolean matchDescription, boolean ignoreHidden)
+ boolean matchDescription, boolean matchFeatureDesc,
+ boolean ignoreHidden)
{
if (residueIndex < 0)
{
@@ -380,6 +407,15 @@ public class Finder implements FinderI
}
else
{
+ if (matchFeatureDesc)
+ {
+ matched = searchSequenceFeatures(residueIndex, searchPattern);
+ if (matched)
+ {
+ return true;
+ }
+ lastFeature = null;
+ }
residueIndex = Integer.MAX_VALUE;
}
}
@@ -543,6 +579,69 @@ public class Finder implements FinderI
}
/**
+ * Searches for a match with the sequence features, and if found, adds the
+ * sequence to the list of match ids, (but not as a duplicate). Answers true
+ * if a match was added, else false.
+ *
+ * @param seq
+ * @param searchPattern
+ * @return
+ */
+ protected boolean searchSequenceFeatures(int from, Regex searchPattern)
+ {
+ if (lastFeatureSequenceIndex != sequenceIndex)
+ {
+ lastFeatureSequenceIndex = sequenceIndex;
+ lastFeature = null;
+ }
+ SequenceI seq = viewport.getAlignment().getSequenceAt(sequenceIndex);
+ SequenceFeaturesI sf = seq.getFeatures();
+
+ // TODO - stash feature list and search incrementally
+ List allFeatures = null;
+ if (frm != null)
+ {
+ allFeatures = frm.findFeaturesAtResidue(seq, seq.getStart(),
+ seq.getEnd());
+ }
+ else
+ {
+ allFeatures = sf.getAllFeatures(null);
+ }
+ // so we can check we are advancing when debugging
+ long fpos = 0;
+
+ for (SequenceFeature feature : allFeatures)
+ {
+ fpos++;
+ if (lastFeature != null)
+ {
+ // iterate till we find last feature matched
+ if (lastFeature != feature)
+ {
+ continue;
+ }
+ else
+ {
+ lastFeature = null;
+ continue;
+ }
+ }
+
+ if (searchPattern.search(feature.type) || (feature.description != null
+ && searchPattern.search(feature.description)))
+ {
+ searchResults.addResult(seq, feature.getBegin(), feature.getEnd());
+ lastFeature = feature;
+ return true;
+ }
+ }
+ residueIndex = Integer.MAX_VALUE;
+ lastFeature = null;
+ return false;
+ }
+
+ /**
* Searches for a match with the sequence description, and if found, adds the
* sequence to the list of match ids (but not as a duplicate). Answers true if
* a match was added, else false.
@@ -634,4 +733,10 @@ public class Finder implements FinderI
{
return searchResults;
}
+
+ @Override
+ public void setFeatureRenderer(FeatureRenderer featureRenderer)
+ {
+ frm = featureRenderer;
+ }
}
diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 58a58e9..3e689d1 100644
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -20,10 +20,10 @@
*/
package jalview.api;
-import jalview.io.DataSourceType;
-
import java.util.List;
+import jalview.io.DataSourceType;
+
/**
* prototype abstract controller for a Jalview alignment view
*
@@ -111,4 +111,12 @@ public interface AlignViewControllerI
boolean markHighlightedColumns(boolean invert, boolean extendCurrent,
boolean toggle);
+ /**
+ * copies each distinct highlighted region on the current view as a new
+ * sequence on the clipboard
+ *
+ * @return
+ */
+ boolean copyHighlightedRegionsToClipboard();
+
}
diff --git a/src/jalview/api/FinderI.java b/src/jalview/api/FinderI.java
index 1d57d81..697072b 100644
--- a/src/jalview/api/FinderI.java
+++ b/src/jalview/api/FinderI.java
@@ -20,11 +20,11 @@
*/
package jalview.api;
+import java.util.List;
+
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;
-import java.util.List;
-
/**
* An interface for searching for a pattern in an aligment
*/
@@ -49,11 +49,13 @@ public interface FinderI
* @param theSearchString
* @param caseSensitive
* @param searchDescription
+ * @param searchFeatureDesc
* @param ignoreHidden
* @return
*/
void findAll(String theSearchString, boolean caseSensitive,
- boolean searchDescription, boolean ignoreHidden);
+ boolean searchDescription, boolean searchFeatureDesc,
+ boolean ignoreHidden);
/**
* Finds the next match for the given search string (interpreted as a regular
@@ -71,11 +73,13 @@ public interface FinderI
* @param theSearchString
* @param caseSensitive
* @param searchDescription
+ * @param searchFeatureDesc
* @param ignoreHidden
* @return
*/
void findNext(String theSearchString, boolean caseSensitive,
- boolean searchDescription, boolean ignoreHidden);
+ boolean searchDescription, boolean searchFeatureDesc,
+ boolean ignoreHidden);
/**
* Returns the (possibly empty) list of sequences matched on sequence name or
@@ -92,4 +96,6 @@ public interface FinderI
*/
SearchResultsI getSearchResults();
+ void setFeatureRenderer(FeatureRenderer featureRenderer);
+
}
\ No newline at end of file
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index 31c914a..167d899 100644
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -20,14 +20,6 @@
*/
package jalview.appletgui;
-import jalview.api.AlignViewportI;
-import jalview.api.FinderI;
-import jalview.datamodel.SearchResultMatchI;
-import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-
import java.awt.Button;
import java.awt.Checkbox;
import java.awt.Font;
@@ -47,6 +39,14 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import jalview.api.AlignViewportI;
+import jalview.api.FinderI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
public class Finder extends Panel implements ActionListener
{
private AlignViewportI av;
@@ -172,12 +172,12 @@ public class Finder extends Panel implements ActionListener
if (doFindAll)
{
finder.findAll(searchString, isCaseSensitive, doSearchDescription,
- false);
+ false, false);
}
else
{
finder.findNext(searchString, isCaseSensitive, doSearchDescription,
- false);
+ false, false);
}
searchResults = finder.getSearchResults();
diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 2fb9cdd..4434331 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -20,6 +20,10 @@
*/
package jalview.controller;
+import java.awt.Color;
+import java.util.BitSet;
+import java.util.List;
+
import jalview.analysis.AlignmentSorter;
import jalview.api.AlignViewControllerGuiI;
import jalview.api.AlignViewControllerI;
@@ -29,19 +33,17 @@ import jalview.api.FeatureRenderer;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.Desktop;
import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
-import java.awt.Color;
-import java.util.BitSet;
-import java.util.List;
-
public class AlignViewController implements AlignViewControllerI
{
AlignViewportI viewport = null;
@@ -471,4 +473,31 @@ public class AlignViewController implements AlignViewControllerI
return false;
}
+ @Override
+ public boolean copyHighlightedRegionsToClipboard()
+ {
+ if (!viewport.hasSearchResults())
+ {
+ // do nothing if no selection exists
+ return false;
+ }
+
+ SearchResultsI searchResults = viewport.getSearchResults();
+ if (searchResults.isEmpty())
+ {
+ return false; // shouldn't happen
+ }
+ List seqs = searchResults.getMatchingSubSequences();
+
+ // TODO: pass in hiddenColumns according to intersection of searchResults
+ // and visible columns. Currently this isn't done, since each contig becomes
+ // a single subsequence
+ Desktop.jalviewClipboard = new Object[] {
+ seqs.toArray(new SequenceI[0]),
+ alignPanel.getAlignment().getDataset(), null };
+ avcg.setStatus(MessageManager.formatMessage(
+ "label.copied_sequences_to_clipboard", seqs.size()));
+ // Technically we should return false, since view has not changed
+ return false;
+ }
}
diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 880f970..909a0fe 100755
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -370,4 +370,27 @@ public class SearchResults implements SearchResultsI
{
matches.addAll(toAdd.getResults());
}
+
+ @Override
+ public List getMatchingSubSequences()
+ {
+ List seqs = new ArrayList<>();
+
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
+ */
+ for (SearchResultMatchI match : matches)
+ {
+ SequenceI seq = match.getSequence();
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ // getSubSequence is index-base0, findIndex returns index-base1
+ seqs.add(seq.getSubSequence(seq.findIndex(match.getStart()) - 1,
+ seq.findIndex(match.getEnd())));
+ }
+ return seqs;
+ }
}
diff --git a/src/jalview/datamodel/SearchResultsI.java b/src/jalview/datamodel/SearchResultsI.java
index c89f363..7946824 100644
--- a/src/jalview/datamodel/SearchResultsI.java
+++ b/src/jalview/datamodel/SearchResultsI.java
@@ -118,4 +118,12 @@ public interface SearchResultsI
* @return number of bits set
*/
int markColumns(SequenceCollectionI sqcol, BitSet bs);
+
+ /**
+ * Return sub-sequences corresponding to distinct contiguous ranges in the
+ * matching set
+ *
+ * @return list of sequence objects
+ */
+ List getMatchingSubSequences();
}
\ No newline at end of file
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e24cbea..032b0bb 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,8 +20,6 @@
*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
@@ -59,6 +57,7 @@ import java.util.Deque;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.List;
+import java.util.Locale;
import java.util.Vector;
import javax.swing.ButtonGroup;
@@ -5829,6 +5828,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
| ActionEvent.CTRL_MASK)) != 0);
}
+ @Override
+ protected void copyHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
+ {
+ avc.copyHighlightedRegionsToClipboard();
+ }
+
/**
* Rebuilds the Colour menu, including any user-defined colours which have
* been loaded either on startup or during the session
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 358d9a4..c40b958 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -20,8 +20,6 @@
*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.Dimension;
import java.awt.event.ActionEvent;
import java.awt.event.FocusAdapter;
@@ -30,6 +28,7 @@ import java.awt.event.KeyEvent;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
@@ -254,6 +253,17 @@ public class Finder extends GFinder
new FeatureEditor(ap, seqs, features, true).showDialog();
}
+ @Override
+ protected void copyToClipboard_actionPerformed()
+ {
+ if (searchResults.isEmpty())
+ {
+ return; // shouldn't happen
+ }
+ // assume viewport controller has same searchResults as we do...
+ ap.alignFrame.avc.copyHighlightedRegionsToClipboard();
+ }
+
/**
* Search the alignment for the next or all matches. If 'all matches', a
* dialog is shown with the number of sequence ids and subsequences matched.
@@ -263,6 +273,7 @@ public class Finder extends GFinder
void doSearch(boolean doFindAll)
{
createFeatures.setEnabled(false);
+ copyToClipboard.setEnabled(false);
String searchString = searchBox.getUserInput();
@@ -283,19 +294,21 @@ public class Finder extends GFinder
finder = new jalview.analysis.Finder(av);
finders.put(av, finder);
}
+ finder.setFeatureRenderer(ap.getFeatureRenderer());
boolean isCaseSensitive = caseSensitive.isSelected();
boolean doSearchDescription = searchDescription.isSelected();
+ boolean doSearchfeatures = searchFeatures.isSelected();
boolean skipHidden = ignoreHidden.isSelected();
if (doFindAll)
{
finder.findAll(searchString, isCaseSensitive, doSearchDescription,
- skipHidden);
+ doSearchfeatures, skipHidden);
}
else
{
finder.findNext(searchString, isCaseSensitive, doSearchDescription,
- skipHidden);
+ doSearchfeatures, skipHidden);
}
searchResults = finder.getSearchResults();
@@ -309,6 +322,7 @@ public class Finder extends GFinder
else
{
createFeatures.setEnabled(true);
+ copyToClipboard.setEnabled(true);
}
searchBox.updateCache();
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 71b6b9e..8ae97b0 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -20,18 +20,6 @@
*/
package jalview.jbgui;
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.GeneticCodeI;
-import jalview.analysis.GeneticCodes;
-import jalview.api.SplitContainerI;
-import jalview.bin.Cache;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.Preferences;
-import jalview.io.FileFormats;
-import jalview.schemes.ResidueColourScheme;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.GridLayout;
@@ -61,6 +49,18 @@ import javax.swing.event.ChangeEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.analysis.GeneticCodeI;
+import jalview.analysis.GeneticCodes;
+import jalview.api.SplitContainerI;
+import jalview.bin.Cache;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.Preferences;
+import jalview.io.FileFormats;
+import jalview.schemes.ResidueColourScheme;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
@SuppressWarnings("serial")
public class GAlignFrame extends JInternalFrame
{
@@ -104,6 +104,8 @@ public class GAlignFrame extends JInternalFrame
JMenuItem copy = new JMenuItem();
+ JMenuItem copyHighlighted = new JMenuItem();
+
JMenuItem cut = new JMenuItem();
JMenu pasteMenu = new JMenu();
@@ -1756,6 +1758,26 @@ public class GAlignFrame extends JInternalFrame
}
};
selectHighlighted.addActionListener(al);
+
+ copyHighlighted = new JMenuItem(
+ MessageManager.getString("action.copy_highlighted_regions"));
+ keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_C,
+ jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx()
+ + jalview.util.ShortcutKeyMaskExWrapper.SHIFT_DOWN_MASK,
+ false);
+ copyHighlighted.setToolTipText(
+ MessageManager.getString("tooltip.copy_highlighted_regions"));
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ copyHighlightedColumns_actionPerformed(actionEvent);
+ }
+ };
+ addMenuActionAndAccelerator(keyStroke, copyHighlighted, al);
+ copyHighlighted.addActionListener(al);
+
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
JMenu autoAnnMenu = new JMenu(
@@ -1806,6 +1828,7 @@ public class GAlignFrame extends JInternalFrame
editMenu.add(redoMenuItem);
editMenu.add(cut);
editMenu.add(copy);
+ editMenu.add(copyHighlighted);
editMenu.add(pasteMenu);
editMenu.add(delete);
editMenu.addSeparator();
@@ -1951,6 +1974,12 @@ public class GAlignFrame extends JInternalFrame
// selectMenu.add(listenToViewSelections);
}
+ protected void copyHighlightedColumns_actionPerformed(
+ ActionEvent actionEvent)
+ {
+
+ }
+
protected void loadVcf_actionPerformed()
{
}
diff --git a/src/jalview/jbgui/GFinder.java b/src/jalview/jbgui/GFinder.java
index c5488f0..9ed2127 100755
--- a/src/jalview/jbgui/GFinder.java
+++ b/src/jalview/jbgui/GFinder.java
@@ -20,13 +20,6 @@
*/
package jalview.jbgui;
-import jalview.datamodel.AlignmentI;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
-import jalview.io.cache.JvCacheableInputBox;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Font;
import java.awt.GridLayout;
@@ -44,6 +37,13 @@ import javax.swing.SwingUtilities;
import javax.swing.event.CaretEvent;
import javax.swing.event.CaretListener;
+import jalview.datamodel.AlignmentI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+import jalview.io.cache.JvCacheableInputBox;
+import jalview.util.MessageManager;
+
public class GFinder extends JPanel
{
private static final java.awt.Font VERDANA_12 = new Font("Verdana",
@@ -59,12 +59,16 @@ public class GFinder extends JPanel
protected JButton createFeatures;
+ protected JButton copyToClipboard;
+
protected JvCacheableInputBox searchBox;
protected JCheckBox caseSensitive;
protected JCheckBox searchDescription;
+ protected JCheckBox searchFeatures;
+
protected JCheckBox ignoreHidden;
public GFinder()
@@ -152,6 +156,10 @@ public class GFinder extends JPanel
searchDescription
.setText(MessageManager.getString("label.include_description"));
+ searchFeatures = new JCheckBox();
+ searchFeatures
+ .setText(MessageManager.getString("label.include_features"));
+
ignoreHidden = new JCheckBox();
ignoreHidden.setText(MessageManager.getString("label.ignore_hidden"));
ignoreHidden.setToolTipText(
@@ -159,6 +167,7 @@ public class GFinder extends JPanel
centrePanel.add(caseSensitive);
centrePanel.add(searchDescription);
+ centrePanel.add(searchFeatures);
centrePanel.add(ignoreHidden);
/*
@@ -198,9 +207,26 @@ public class GFinder extends JPanel
createFeatures_actionPerformed();
}
});
+ copyToClipboard = new JButton();
+ copyToClipboard.setEnabled(false);
+ copyToClipboard.setFont(VERDANA_12);
+ copyToClipboard.setText(MessageManager.getString("label.copy"));
+ copyToClipboard.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ copyToClipboard_actionPerformed();
+ }
+ });
eastPanel.add(findNext);
eastPanel.add(findAll);
eastPanel.add(createFeatures);
+ eastPanel.add(copyToClipboard);
+ }
+
+ protected void copyToClipboard_actionPerformed()
+ {
}
protected void textfield_keyPressed(KeyEvent e)
diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 7e3bd86..0220c36 100644
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -24,6 +24,12 @@ import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertSame;
import static org.testng.Assert.assertTrue;
+import java.util.List;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.bin.Cache;
@@ -34,19 +40,14 @@ import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
-
-import java.util.List;
-
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
import junit.extensions.PA;
public class FinderTest
@@ -82,6 +83,12 @@ public class FinderTest
DataSourceType.PASTE);
av = af.getViewport();
al = av.getAlignment();
+ al.getSequenceAt(0).addSequenceFeature(
+ new SequenceFeature("BBBB", "FeatureB", 9, 11, ""));
+ al.getSequenceAt(3).addSequenceFeature(
+ new SequenceFeature("BBAB", "FeatureA", 1, 3, ""));
+ al.getSequenceAt(3).addSequenceFeature(
+ new SequenceFeature("AAAA", "FeatureA", 9, 11, ""));
}
@AfterMethod(alwaysRun = true)
@@ -100,7 +107,7 @@ public class FinderTest
* find next match only
*/
Finder f = new Finder(av);
- f.findNext("E.H", false, false, false); // 'E, any character, H'
+ f.findNext("E.H", false, false, false, false); // 'E, any character, H'
// should match seq2 efH only
SearchResultsI sr = f.getSearchResults();
assertEquals(sr.getCount(), 1);
@@ -110,7 +117,7 @@ public class FinderTest
assertEquals(matches.get(0).getEnd(), 7);
f = new Finder(av);
- f.findAll("E.H", false, false, false); // 'E, any character, H'
+ f.findAll("E.H", false, false, false, false); // 'E, any character, H'
// should match seq2 efH and seq3 EFH
sr = f.getSearchResults();
assertEquals(sr.getCount(), 2);
@@ -131,7 +138,7 @@ public class FinderTest
* single symbol should find *all* matching symbols
*/
Finder f = new Finder(av);
- f.findAll("M", false, false, false);
+ f.findAll("M", false, false, false, false);
SearchResultsI sr = f.getSearchResults();
assertEquals(sr.getCount(), 5);
@@ -148,7 +155,7 @@ public class FinderTest
/*
* find first match should return seq1 residue 9
*/
- f.findNext("9", false, false, false);
+ f.findNext("9", false, false, false, false);
SearchResultsI sr = f.getSearchResults();
assertEquals(sr.getCount(), 1);
List matches = sr.getResults();
@@ -163,7 +170,7 @@ public class FinderTest
f = new Finder(av);
String name = al.getSequenceAt(0).getName();
al.getSequenceAt(0).setName("Q9XA0");
- f.findAll("9", false, false, false);
+ f.findAll("9", false, false, false, false);
sr = f.getSearchResults();
assertEquals(sr.getCount(), 2);
matches = sr.getResults();
@@ -179,7 +186,7 @@ public class FinderTest
* parsing of search string as integer is strict
*/
f = new Finder(av);
- f.findNext(" 9", false, false, false);
+ f.findNext(" 9", false, false, false, false);
assertTrue(f.getSearchResults().isEmpty());
}
@@ -196,7 +203,7 @@ public class FinderTest
Finder f = new Finder(av);
PA.setValue(f, "sequenceIndex", 1);
PA.setValue(f, "residueIndex", -1);
- f.findNext("e", false, false, false); // matches id
+ f.findNext("e", false, false, false, false); // matches id
assertTrue(f.getSearchResults().isEmpty());
assertEquals(f.getIdMatches().size(), 1);
@@ -208,7 +215,7 @@ public class FinderTest
f = new Finder(av);
PA.setValue(f, "sequenceIndex", 1);
PA.setValue(f, "residueIndex", 0);
- f.findNext("e", false, false, false); // matches in sequence
+ f.findNext("e", false, false, false, false); // matches in sequence
assertTrue(f.getIdMatches().isEmpty());
assertEquals(f.getSearchResults().getCount(), 1);
List matches = f.getSearchResults().getResults();
@@ -224,7 +231,7 @@ public class FinderTest
f = new Finder(av);
PA.setValue(f, "sequenceIndex", 1);
PA.setValue(f, "residueIndex", 7);
- f.findNext("e", false, false, false);
+ f.findNext("e", false, false, false, false);
assertEquals(f.getIdMatches().size(), 1);
assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
assertTrue(f.getSearchResults().isEmpty());
@@ -246,7 +253,7 @@ public class FinderTest
* find first match only
*/
Finder f = new Finder(av2);
- f.findNext("rAF", false, true, false);
+ f.findNext("rAF", false, true, false, false);
assertEquals(f.getIdMatches().size(), 1);
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertTrue(f.getSearchResults().isEmpty());
@@ -255,7 +262,7 @@ public class FinderTest
* find all matches
*/
f = new Finder(av2);
- f.findAll("rAF", false, true, false);
+ f.findAll("rAF", false, true, false, false);
assertEquals(f.getIdMatches().size(), 2);
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -265,7 +272,7 @@ public class FinderTest
* case sensitive
*/
f = new Finder(av2);
- f.findAll("RAF", true, true, false);
+ f.findAll("RAF", true, true, false, false);
assertEquals(f.getIdMatches().size(), 1);
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertTrue(f.getSearchResults().isEmpty());
@@ -281,7 +288,7 @@ public class FinderTest
/*
* sequence matches should have no duplicates
*/
- f.findAll("EFH", false, true, false);
+ f.findAll("EFH", false, true, false, false);
assertEquals(f.getIdMatches().size(), 2);
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -309,7 +316,7 @@ public class FinderTest
* case insensitive; seq1 occurs twice in sequence id but
* only one match should be returned
*/
- f.findAll("SEQ1", false, false, false);
+ f.findAll("SEQ1", false, false, false, false);
assertEquals(f.getIdMatches().size(), 1);
assertSame(f.getIdMatches().get(0), al.getSequenceAt(0));
SearchResultsI searchResults = f.getSearchResults();
@@ -319,7 +326,7 @@ public class FinderTest
* case sensitive
*/
f = new Finder(av);
- f.findAll("SEQ1", true, false, false);
+ f.findAll("SEQ1", true, false, false, false);
searchResults = f.getSearchResults();
assertTrue(searchResults.isEmpty());
@@ -330,7 +337,7 @@ public class FinderTest
AlignViewportI av2 = new AlignViewport(al2);
al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
f = new Finder(av2);
- f.findAll("ABZ", false, false, false);
+ f.findAll("ABZ", false, false, false, false);
assertEquals(f.getIdMatches().size(), 1);
assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
searchResults = f.getSearchResults();
@@ -359,7 +366,7 @@ public class FinderTest
* efh should be matched in seq2 only
*/
FinderI f = new Finder(av);
- f.findNext("EfH", false, false, false);
+ f.findNext("EfH", false, false, false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
@@ -371,7 +378,7 @@ public class FinderTest
* I should be found in seq1 (twice) and seq2 (once)
*/
f = new Finder(av);
- f.findNext("I", false, false, false); // find next: seq1/16
+ f.findNext("I", false, false, false, false); // find next: seq1/16
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
@@ -379,7 +386,7 @@ public class FinderTest
assertEquals(match.getStart(), 16);
assertEquals(match.getEnd(), 16);
- f.findNext("I", false, false, false); // find next: seq1/18
+ f.findNext("I", false, false, false, false); // find next: seq1/18
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
@@ -387,7 +394,7 @@ public class FinderTest
assertEquals(match.getStart(), 18);
assertEquals(match.getEnd(), 18);
- f.findNext("I", false, false, false); // find next: seq2/8
+ f.findNext("I", false, false, false, false); // find next: seq2/8
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
@@ -395,13 +402,13 @@ public class FinderTest
assertEquals(match.getStart(), 8);
assertEquals(match.getEnd(), 8);
- f.findNext("I", false, false, false);
+ f.findNext("I", false, false, false, false);
assertTrue(f.getSearchResults().isEmpty());
/*
* find should reset to start of alignment after a failed search
*/
- f.findNext("I", false, false, false); // find next: seq1/16
+ f.findNext("I", false, false, false, false); // find next: seq1/16
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
@@ -418,7 +425,7 @@ public class FinderTest
public void testFindAll_maximalResultOnly()
{
Finder f = new Finder(av);
- f.findAll("M+", false, false, false);
+ f.findAll("M+", false, false, false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
SearchResultMatchI match = searchResults.getResults().get(0);
@@ -434,7 +441,7 @@ public class FinderTest
public void testFindAll()
{
Finder f = new Finder(av);
- f.findAll("EfH", false, false, false);
+ f.findAll("EfH", false, false, false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
@@ -449,7 +456,7 @@ public class FinderTest
/*
* find all I should find 2 positions in seq1, 1 in seq2
*/
- f.findAll("I", false, false, false);
+ f.findAll("I", false, false, false, false);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 3);
match = searchResults.getResults().get(0);
@@ -477,7 +484,7 @@ public class FinderTest
/*
* BC should match seq1/9-10 and seq2/2-3
*/
- f.findAll("BC", true, false, false);
+ f.findAll("BC", true, false, false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
@@ -493,7 +500,7 @@ public class FinderTest
* bc should match seq3/1-2
*/
f = new Finder(av);
- f.findAll("bc", true, false, false);
+ f.findAll("bc", true, false, false, false);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
@@ -501,7 +508,7 @@ public class FinderTest
assertEquals(match.getStart(), 1);
assertEquals(match.getEnd(), 2);
- f.findAll("bC", true, false, false);
+ f.findAll("bC", true, false, false, false);
assertTrue(f.getSearchResults().isEmpty());
}
@@ -524,7 +531,7 @@ public class FinderTest
av.setSelectionGroup(sg);
FinderI f = new Finder(av);
- f.findNext("b", false, false, false);
+ f.findNext("b", false, false, false, false);
assertTrue(f.getIdMatches().isEmpty());
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
@@ -536,12 +543,12 @@ public class FinderTest
/*
* a second Find should not return the 'b' in seq3 as outside the selection
*/
- f.findNext("b", false, false, false);
+ f.findNext("b", false, false, false, false);
assertTrue(f.getSearchResults().isEmpty());
assertTrue(f.getIdMatches().isEmpty());
f = new Finder(av);
- f.findNext("d", false, false, false);
+ f.findNext("d", false, false, false, false);
assertTrue(f.getIdMatches().isEmpty());
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
@@ -549,7 +556,7 @@ public class FinderTest
assertSame(match.getSequence(), al.getSequenceAt(1));
assertEquals(match.getStart(), 4);
assertEquals(match.getEnd(), 4);
- f.findNext("d", false, false, false);
+ f.findNext("d", false, false, false, false);
assertTrue(f.getIdMatches().isEmpty());
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
@@ -581,7 +588,7 @@ public class FinderTest
* search for 'e' should match two sequence ids and one residue
*/
Finder f = new Finder(av);
- f.findAll("e", false, false, false);
+ f.findAll("e", false, false, false, false);
assertEquals(f.getIdMatches().size(), 2);
assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -596,7 +603,7 @@ public class FinderTest
* search for 'Q' should match two sequence ids only
*/
f = new Finder(av);
- f.findAll("Q", false, false, false);
+ f.findAll("Q", false, false, false, false);
assertEquals(f.getIdMatches().size(), 2);
assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -627,7 +634,7 @@ public class FinderTest
* search for 'I' should match two sequence positions
*/
Finder f = new Finder(av);
- f.findAll("I", false, false, false);
+ f.findAll("I", false, false, false, false);
assertTrue(f.getIdMatches().isEmpty());
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
@@ -664,7 +671,7 @@ public class FinderTest
hc.hideColumns(3, 3);
al.setHiddenColumns(hc);
Finder f = new Finder(av);
- f.findAll("aaa", false, false, false);
+ f.findAll("aaa", false, false, false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
@@ -686,7 +693,7 @@ public class FinderTest
* find the visible D in seq2
*/
f = new Finder(av);
- f.findAll("D", false, false, false);
+ f.findAll("D", false, false, false, false);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
@@ -699,7 +706,7 @@ public class FinderTest
* consecutive in the visible columns
*/
f = new Finder(av);
- f.findAll("AD", false, false, false);
+ f.findAll("AD", false, false, false, false);
searchResults = f.getSearchResults();
assertTrue(searchResults.isEmpty());
@@ -708,7 +715,7 @@ public class FinderTest
* (first run includes hidden gaps)
*/
f = new Finder(av);
- f.findAll("aaa", false, false, false);
+ f.findAll("aaa", false, false, false, false);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
match = searchResults.getResults().get(0);
@@ -727,7 +734,7 @@ public class FinderTest
*/
hc.hideColumns(2, 5);
f = new Finder(av);
- f.findAll("aaa", false, false, false);
+ f.findAll("aaa", false, false, false, false);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
match = searchResults.getResults().get(0);
@@ -742,7 +749,7 @@ public class FinderTest
/*
* find all 'BE' should not match across hidden columns in seq1
*/
- f.findAll("BE", false, false, false);
+ f.findAll("BE", false, false, false, false);
assertTrue(f.getSearchResults().isEmpty());
/*
@@ -752,7 +759,7 @@ public class FinderTest
hc.revealAllHiddenColumns(new ColumnSelection());
hc.hideColumns(8, 13);
f = new Finder(av);
- f.findNext("H", false, false, false);
+ f.findNext("H", false, false, false, false);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
match = searchResults.getResults().get(0);
@@ -795,7 +802,7 @@ public class FinderTest
* should match seq2/1, seq2/7, not seq3/6
*/
Finder f = new Finder(av);
- f.findAll("[AH]", false, false, false);
+ f.findAll("[AH]", false, false, false, false);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
@@ -832,7 +839,7 @@ public class FinderTest
* aaaMMMMaaa
*/
Finder f = new Finder(av);
- f.findAll("abe", false, false, true); // true = ignore hidden
+ f.findAll("abe", false, false, false, true); // true = ignore hidden
SearchResultsI searchResults = f.getSearchResults();
/*
@@ -851,7 +858,7 @@ public class FinderTest
assertEquals(match.getEnd(), 12);
f = new Finder(av);
- f.findNext("a.E", false, false, true);
+ f.findNext("a.E", false, false, false, true);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
assertEquals(searchResults.getResults().size(), 2);
@@ -864,7 +871,7 @@ public class FinderTest
assertEquals(match.getStart(), 12); // E
assertEquals(match.getEnd(), 12);
- f.findNext("a.E", false, false, true);
+ f.findNext("a.E", false, false, false, true);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
assertEquals(searchResults.getResults().size(), 2);
@@ -881,7 +888,7 @@ public class FinderTest
* find all matching across two hidden column regions
* note one 'match' is returned as three contiguous matches
*/
- f.findAll("BEG", false, false, true);
+ f.findAll("BEG", false, false, false, true);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
assertEquals(searchResults.getResults().size(), 3);
@@ -908,7 +915,7 @@ public class FinderTest
selection.setEndRes(9);
al.getSequences().forEach(seq -> selection.addSequence(seq, false));
av.setSelectionGroup(selection);
- f.findAll("A.*H", false, false, true);
+ f.findAll("A.*H", false, false, false, true);
searchResults = f.getSearchResults();
assertEquals(searchResults.getCount(), 1);
assertEquals(searchResults.getResults().size(), 3);
@@ -926,4 +933,60 @@ public class FinderTest
assertEquals(match.getStart(), 7); // H (there is no G)
assertEquals(match.getEnd(), 7);
}
+
+ @Test(groups = "Functional")
+ public void testFind_featuresOnly()
+ {
+ Finder f = new Finder(av);
+ // no match when not searching feature descriptions
+ f.findAll("Feature", false, false, false, true);
+ assertEquals(f.getSearchResults().getCount(), 0);
+
+ // no match when case sensitive on feature descriptions
+ f.findAll("feature", true, false, true, true);
+ assertEquals(f.getSearchResults().getCount(), 0);
+
+ // search feature descriptions - all match
+ f.findAll("Feature", false, false, true, true);
+ assertEquals(f.getSearchResults().getCount(), 3);
+
+ List seqs = f.getSearchResults().getMatchingSubSequences();
+ // assume order is preserved in results
+ assertEquals(al.getSequenceAt(0).getDatasetSequence(),
+ seqs.get(0).getDatasetSequence());
+ assertEquals(seqs.get(0).getStart(), 9);
+ assertEquals(seqs.get(0).getEnd(), 11);
+ assertEquals(al.getSequenceAt(3).getDatasetSequence(),
+ seqs.get(1).getDatasetSequence());
+ assertEquals(seqs.get(1).getStart(), 9);
+ assertEquals(seqs.get(1).getEnd(), 11);
+ assertEquals(al.getSequenceAt(3).getDatasetSequence(),
+ seqs.get(2).getDatasetSequence());
+ assertEquals(seqs.get(2).getStart(), 1);
+ assertEquals(seqs.get(2).getEnd(), 3);
+
+ SequenceI sq = null;
+ // search feature descriptions incrementally
+ // assume same order as before
+ f.findNext("Feature", false, false, true, true);
+ assertEquals(f.getSearchResults().getCount(), 1);
+ sq = f.getSearchResults().getMatchingSubSequences().get(0);
+ assertEquals(sq.getSequenceAsString(),
+ seqs.get(0).getSequenceAsString());
+
+ // ..
+ f.findNext("Feature", false, false, true, true);
+ assertEquals(f.getSearchResults().getCount(), 1);
+ sq = f.getSearchResults().getMatchingSubSequences().get(0);
+ assertEquals(sq.getSequenceAsString(),
+ seqs.get(1).getSequenceAsString());
+
+ // ..
+ f.findNext("Feature", false, false, true, true);
+ assertEquals(f.getSearchResults().getCount(), 1);
+ sq = f.getSearchResults().getMatchingSubSequences().get(0);
+ assertEquals(sq.getSequenceAsString(),
+ seqs.get(2).getSequenceAsString());
+
+ }
}
diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index ca3b55c..e8e0bb1 100644
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -23,6 +23,13 @@ package jalview.controller;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.BitSet;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
import jalview.analysis.Finder;
import jalview.api.AlignViewControllerI;
import jalview.api.FeatureColourI;
@@ -40,13 +47,6 @@ import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.schemes.FeatureColour;
-import java.awt.Color;
-import java.util.Arrays;
-import java.util.BitSet;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
public class AlignViewControllerTest
{
@@ -226,7 +226,7 @@ public class AlignViewControllerTest
* test Match/Find works first
*/
FinderI f = new Finder(af.getViewport());
- f.findAll("M+", true, false, false);
+ f.findAll("M+", true, false, false, false);
assertEquals(
"Finder found different set of results to manually created SearchResults",
sr, f.getSearchResults());
diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index 5d2b8a4..b1bb43c 100644
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
import java.util.BitSet;
+import java.util.List;
import org.junit.Assert;
import org.testng.annotations.BeforeClass;
@@ -369,4 +370,44 @@ public class SearchResultsTest
sr.addResult(cds2, 7, 9); // start-end overlap
assertTrue(sr.involvesSequence(cds2));
}
+
+ /**
+ * Test extraction of Sequence objects for matched ranges on a sequence
+ */
+ @Test(groups = { "Functional" })
+ public void testGetSequences()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SequenceI seq2 = new Sequence("", "nopqrstuvwxyz");
+ seq2.setStart(23);
+ seq2.setEnd(35);
+ List seqres = null;
+
+ SearchResultsI sr = new SearchResults();
+ seqres = sr.getMatchingSubSequences();
+ assertEquals(0, seqres.size());
+
+ sr.addResult(seq1, 3, 5);
+ seqres = sr.getMatchingSubSequences();
+
+ assertEquals(1, seqres.size());
+ assertEquals("cde", seqres.get(0).getSequenceAsString());
+ assertEquals(3, seqres.get(0).getStart());
+ assertEquals(seq1, seqres.get(0).getDatasetSequence());
+
+ sr.addResult(seq1, 3, 6);
+ seqres = sr.getMatchingSubSequences();
+
+ assertEquals(2, seqres.size());
+ assertEquals("cdef", seqres.get(1).getSequenceAsString());
+ assertEquals(3, seqres.get(1).getStart());
+
+ // this is a quirk - match on 26-29 yields subsequence 27-30
+ sr.addResult(seq2, 26, 29);
+ seqres = sr.getMatchingSubSequences();
+ assertEquals(3, seqres.size());
+ assertEquals("qrst", seqres.get(2).getSequenceAsString());
+ assertEquals(26, seqres.get(2).getStart());
+ }
+
}
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