X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=11321eba1b1f91c37fa36065fb6add400ec681c2;hb=9201765247470c08d366abef2713c1c736adf2cb;hp=d559d17f9aae64e21d961461bcaaf1ce50ddd80e;hpb=1e085f14ae2f19adfac0153c437ee891f0ad07bc;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d559d17..11321eb 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,6 +1,6 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * 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.
*
@@ -18,24 +18,6 @@
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-/*
- * 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
- */
package jalview.gui;
import jalview.analysis.AlignmentUtils;
@@ -43,6 +25,9 @@ import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
@@ -52,17 +37,21 @@ import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShader;
+import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ResidueColourScheme;
import jalview.schemes.UserColourScheme;
-import jalview.structure.CommandListener;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
import jalview.ws.params.AutoCalcSetting;
import java.awt.Container;
@@ -72,11 +61,9 @@ import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
-import java.util.Set;
import java.util.Vector;
import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
/**
* DOCUMENT ME!
@@ -85,7 +72,7 @@ import javax.swing.JOptionPane;
* @version $Revision: 1.141 $
*/
public class AlignViewport extends AlignmentViewport implements
- SelectionSource, CommandListener
+ SelectionSource
{
Font font;
@@ -251,10 +238,7 @@ public class AlignViewport extends AlignmentViewport implements
void init()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
+ ranges = new ViewportRanges(this.alignment);
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -299,28 +283,27 @@ public class AlignViewport extends AlignmentViewport implements
initAutoAnnotation();
String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
: Preferences.DEFAULT_COLOUR_PROT;
- String propertyValue = Cache.getProperty(colourProperty);
- if (propertyValue == null)
+ String schemeName = Cache.getProperty(colourProperty);
+ if (schemeName == null)
{
- // fall back on this property for backwards compatibility
- propertyValue = Cache.getProperty(Preferences.DEFAULT_COLOUR);
+ // only DEFAULT_COLOUR available in Jalview before 2.9
+ schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
}
- if (propertyValue != null)
- {
- globalColourScheme = ColourSchemeProperty.getColour(alignment,
- propertyValue);
+ ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(
+ alignment, schemeName);
+ residueShading = new ResidueShader(colourScheme);
- if (globalColourScheme instanceof UserColourScheme)
- {
- globalColourScheme = UserDefinedColours.loadDefaultColours();
- ((UserColourScheme) globalColourScheme).setThreshold(0,
- isIgnoreGapsConsensus());
- }
+ if (colourScheme instanceof UserColourScheme)
+ {
+ residueShading = new ResidueShader(
+ UserDefinedColours.loadDefaultColours());
+ residueShading.setThreshold(0, isIgnoreGapsConsensus());
+ }
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
+ if (residueShading != null)
+ {
+ residueShading.setConsensus(hconsensus);
}
}
@@ -398,7 +381,6 @@ public class AlignViewport extends AlignmentViewport implements
super.setViewStyle(settingsForView);
setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
viewStyle.getFontSize()), false);
-
}
/**
@@ -417,10 +399,11 @@ public class AlignViewport extends AlignmentViewport implements
* @param align
* DOCUMENT ME!
*/
+ @Override
public void setAlignment(AlignmentI align)
{
replaceMappings(align);
- this.alignment = align;
+ super.setAlignment(align);
}
/**
@@ -461,7 +444,7 @@ public class AlignViewport extends AlignmentViewport implements
AlignmentI al = getAlignment();
if (al != null)
{
- Set mappings = al.getCodonFrames();
+ List mappings = al.getCodonFrames();
if (mappings != null)
{
StructureSelectionManager ssm = StructureSelectionManager
@@ -482,6 +465,7 @@ public class AlignViewport extends AlignmentViewport implements
*
* @return DOCUMENT ME!
*/
+ @Override
public char getGapCharacter()
{
return getAlignment().getGapCharacter();
@@ -504,16 +488,6 @@ public class AlignViewport extends AlignmentViewport implements
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
- */
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- /**
- * DOCUMENT ME!
- *
* @param tree
* DOCUMENT ME!
*/
@@ -617,6 +591,7 @@ public class AlignViewport extends AlignmentViewport implements
/**
* Send the current selection to be broadcast to any selection listeners.
*/
+ @Override
public void sendSelection()
{
jalview.structure.StructureSelectionManager
@@ -658,39 +633,6 @@ public class AlignViewport extends AlignmentViewport implements
}
/**
- * synthesize a column selection if none exists so it covers the given
- * selection group. if wholewidth is false, no column selection is made if the
- * selection group covers the whole alignment width.
- *
- * @param sg
- * @param wholewidth
- */
- public void expandColSelection(SequenceGroup sg, boolean wholewidth)
- {
- int sgs, sge;
- if (sg != null
- && (sgs = sg.getStartRes()) >= 0
- && sg.getStartRes() <= (sge = sg.getEndRes())
- && (colSel == null || colSel.getSelected() == null || colSel
- .getSelected().size() == 0))
- {
- if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
- {
- // do nothing
- return;
- }
- if (colSel == null)
- {
- colSel = new ColumnSelection();
- }
- for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
- {
- colSel.addElement(cspos);
- }
- }
- }
-
- /**
* Returns the (Desktop) instance of the StructureSelectionManager
*/
@Override
@@ -711,31 +653,49 @@ public class AlignViewport extends AlignmentViewport implements
List seqvectors = new ArrayList();
for (PDBEntry pdb : pdbEntries)
{
- List seqs = new ArrayList();
+ List choosenSeqs = new ArrayList();
for (SequenceI sq : alignment.getSequences())
{
- Vector pdbs = sq.getDatasetSequence().getAllPDBEntries();
- if (pdbs == null)
+ Vector pdbRefEntries = sq.getDatasetSequence()
+ .getAllPDBEntries();
+ if (pdbRefEntries == null)
{
continue;
}
- for (PDBEntry p1 : pdbs)
+ for (PDBEntry pdbRefEntry : pdbRefEntries)
{
- if (p1.getId().equals(pdb.getId()))
+ if (pdbRefEntry.getId().equals(pdb.getId()))
{
- if (!seqs.contains(sq))
+ if (pdbRefEntry.getChainCode() != null
+ && pdb.getChainCode() != null)
{
- seqs.add(sq);
- continue;
+ if (pdbRefEntry.getChainCode().equalsIgnoreCase(
+ pdb.getChainCode())
+ && !choosenSeqs.contains(sq))
+ {
+ choosenSeqs.add(sq);
+ continue;
+ }
}
+ else
+ {
+ if (!choosenSeqs.contains(sq))
+ {
+ choosenSeqs.add(sq);
+ continue;
+ }
+ }
+
}
}
}
- seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
+ seqvectors
+ .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
}
return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
}
+ @Override
public boolean isNormaliseSequenceLogo()
{
return normaliseSequenceLogo;
@@ -750,6 +710,7 @@ public class AlignViewport extends AlignmentViewport implements
*
* @return true if alignment characters should be displayed
*/
+ @Override
public boolean isValidCharWidth()
{
return validCharWidth;
@@ -825,10 +786,10 @@ public class AlignViewport extends AlignmentViewport implements
* may give the user the option to open a new frame, or split panel, with cDNA
* and protein linked.
*
- * @param al
+ * @param toAdd
* @param title
*/
- public void addAlignment(AlignmentI al, String title)
+ public void addAlignment(AlignmentI toAdd, String title)
{
// TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
@@ -841,25 +802,26 @@ public class AlignViewport extends AlignmentViewport implements
// TODO: create undo object for this JAL-1101
/*
- * If any cDNA/protein mappings can be made between the alignments, offer to
- * open a linked alignment with split frame option.
+ * Ensure datasets are created for the new alignment as
+ * mappings operate on dataset sequences
+ */
+ toAdd.setDataset(null);
+
+ /*
+ * Check if any added sequence could be the object of a mapping or
+ * cross-reference; if so, make the mapping explicit
+ */
+ getAlignment().realiseMappings(toAdd.getSequences());
+
+ /*
+ * If any cDNA/protein mappings exist or can be made between the alignments,
+ * offer to open a split frame with linked alignments
*/
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
- if (al.getDataset() == null)
- {
- // need to create ds seqs
- for (SequenceI sq : al.getSequences())
- {
- if (sq.getDatasetSequence() == null)
- {
- sq.createDatasetSequence();
- }
- }
- }
- if (AlignmentUtils.isMappable(al, getAlignment()))
+ if (AlignmentUtils.isMappable(toAdd, getAlignment()))
{
- if (openLinkedAlignment(al, title))
+ if (openLinkedAlignment(toAdd, title))
{
return;
}
@@ -872,9 +834,22 @@ public class AlignViewport extends AlignmentViewport implements
// TODO: JAL-407 regardless of above - identical sequences (based on ID and
// provenance) should share the same dataset sequence
- for (int i = 0; i < al.getHeight(); i++)
+ AlignmentI al = getAlignment();
+ String gap = String.valueOf(al.getGapCharacter());
+ for (int i = 0; i < toAdd.getHeight(); i++)
{
- getAlignment().addSequence(al.getSequenceAt(i));
+ SequenceI seq = toAdd.getSequenceAt(i);
+ /*
+ * experimental!
+ * - 'align' any mapped sequences as per existing
+ * e.g. cdna to genome, domain hit to protein sequence
+ * very experimental! (need a separate menu option for this)
+ * - only add mapped sequences ('select targets from a dataset')
+ */
+ if (true /*AlignmentUtils.alignSequenceAs(seq, al, gap, true, true)*/)
+ {
+ al.addSequence(seq);
+ }
}
setEndSeq(getAlignment().getHeight());
@@ -898,9 +873,9 @@ public class AlignViewport extends AlignmentViewport implements
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
- int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
MessageManager.getString("label.open_split_window"),
- JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
options, options[0]);
if (response != 1 && response != 2)
@@ -940,7 +915,7 @@ public class AlignViewport extends AlignmentViewport implements
// TODO if we want this (e.g. to enable reload of the alignment from file),
// we will need to add parameters to the stack.
- // if (!protocol.equals(AppletFormatAdapter.PASTE))
+ // if (!protocol.equals(DataSourceType.PASTE))
// {
// alignFrame.setFileName(file, format);
// }
@@ -1065,14 +1040,14 @@ public class AlignViewport extends AlignmentViewport implements
* there is no complement, or it is not following highlights, or no mapping
* is found, the result will be empty.
*/
- SearchResults sr = new SearchResults();
+ SearchResultsI sr = new SearchResults();
int verticalOffset = findComplementScrollTarget(sr);
if (!sr.isEmpty())
{
// TODO would like next line without cast but needs more refactoring...
final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
.getAlignPanel();
- complementPanel.setFollowingComplementScroll(true);
+ complementPanel.setDontScrollComplement(true);
complementPanel.scrollToCentre(sr, verticalOffset);
}
}
@@ -1107,4 +1082,68 @@ public class AlignViewport extends AlignmentViewport implements
return true;
}
+ /**
+ * Applies the supplied feature settings descriptor to currently known
+ * features. This supports an 'initial configuration' of feature colouring
+ * based on a preset or user favourite. This may then be modified in the usual
+ * way using the Feature Settings dialogue.
+ *
+ * @param featureSettings
+ */
+ @Override
+ public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
+ {
+ if (featureSettings == null)
+ {
+ return;
+ }
+
+ FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+ fr.findAllFeatures(true);
+ List renderOrder = fr.getRenderOrder();
+ FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
+ displayed.clear();
+ // TODO this clears displayed.featuresRegistered - do we care?
+
+ /*
+ * set feature colour if specified by feature settings
+ * set visibility of all features
+ */
+ for (String type : renderOrder)
+ {
+ FeatureColourI preferredColour = featureSettings
+ .getFeatureColour(type);
+ if (preferredColour != null)
+ {
+ fr.setColour(type, preferredColour);
+ }
+ if (featureSettings.isFeatureDisplayed(type))
+ {
+ displayed.setVisible(type);
+ }
+ }
+
+ /*
+ * set visibility of feature groups
+ */
+ for (String group : fr.getFeatureGroups())
+ {
+ fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
+ }
+
+ /*
+ * order the features
+ */
+ if (featureSettings.optimiseOrder())
+ {
+ // TODO not supported (yet?)
+ }
+ else
+ {
+ fr.orderFeatures(featureSettings);
+ }
+ fr.setTransparency(featureSettings.getTransparency());
+ }
+
}