X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=a8bc815a62a6bbf3c668159bf337095c3ba86922;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=b1a4fee90d33aae9fbd2b05c0816979559225419;hpb=4316d20b437d529be1d9ddafc0118fadd1b6a4ce;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index b1a4fee..a8bc815 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -18,29 +18,22 @@
* 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 java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Rectangle;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+
import jalview.analysis.AlignmentUtils;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureColourI;
@@ -48,58 +41,56 @@ import jalview.api.FeatureSettingsModelI;
import jalview.api.FeaturesDisplayedI;
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
+import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResults;
-import jalview.datamodel.Sequence;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.io.IdentifyFile;
+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.ColorUtils;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision: 1.141 $
*/
-public class AlignViewport extends AlignmentViewport implements
- SelectionSource, CommandListener
+public class AlignViewport extends AlignmentViewport
+ implements SelectionSource
{
Font font;
- NJTree currentTree = null;
-
boolean cursorMode = false;
boolean antiAlias = false;
- private Rectangle explodedGeometry;
+ private Rectangle explodedGeometry = null;
- String viewName;
+ private String viewName = null;
/*
* Flag set true on the view that should 'gather' multiple views of the same
@@ -120,7 +111,7 @@ public class AlignViewport extends AlignmentViewport implements
*/
public AlignViewport(AlignmentI al)
{
- setAlignment(al);
+ super(al);
init();
}
@@ -138,20 +129,21 @@ public class AlignViewport extends AlignmentViewport implements
public AlignViewport(AlignmentI al, String seqsetid, String viewid)
{
+ super(al);
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug("Setting viewport's sequence set id : "
- + sequenceSetID);
+ Console.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Console.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
init();
+
}
/**
@@ -162,12 +154,12 @@ public class AlignViewport extends AlignmentViewport implements
* @param hiddenColumns
* ColumnSelection
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns)
{
- setAlignment(al);
+ super(al);
if (hiddenColumns != null)
{
- colSel = hiddenColumns;
+ al.setHiddenColumns(hiddenColumns);
}
init();
}
@@ -180,7 +172,7 @@ public class AlignViewport extends AlignmentViewport implements
* @param seqsetid
* (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
String seqsetid)
{
this(al, hiddenColumns, seqsetid, null);
@@ -196,25 +188,26 @@ public class AlignViewport extends AlignmentViewport implements
* @param viewid
* (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns,
String seqsetid, String viewid)
{
+ super(al);
sequenceSetID = seqsetid;
viewId = viewid;
// TODO remove these once 2.4.VAMSAS release finished
- if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ if (seqsetid != null)
{
- Cache.log.debug("Setting viewport's sequence set id : "
- + sequenceSetID);
+ Console.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
- if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
+ if (viewId != null)
{
- Cache.log.debug("Setting viewport's view id : " + viewId);
+ Console.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
+
if (hiddenColumns != null)
{
- colSel = hiddenColumns;
+ al.setHiddenColumns(hiddenColumns);
}
init();
}
@@ -224,7 +217,7 @@ public class AlignViewport extends AlignmentViewport implements
*/
private void applyViewProperties()
{
- antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+ antiAlias = Cache.getDefault("ANTI_ALIAS", true);
viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
@@ -238,25 +231,21 @@ public class AlignViewport extends AlignmentViewport implements
setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true));
viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true));
viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false));
- viewStyle.setShowUnconserved(Cache
- .getDefault("SHOW_UNCONSERVED", false));
+ viewStyle.setShowUnconserved(
+ Cache.getDefault("SHOW_UNCONSERVED", false));
sortByTree = Cache.getDefault("SORT_BY_TREE", false);
followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true);
- sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault(
- Preferences.SORT_ANNOTATIONS,
- SequenceAnnotationOrder.NONE.name()));
- showAutocalculatedAbove = Cache.getDefault(
- Preferences.SHOW_AUTOCALC_ABOVE, false);
- viewStyle.setScaleProteinAsCdna(Cache.getDefault(
- Preferences.SCALE_PROTEIN_TO_CDNA, true));
+ sortAnnotationsBy = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ showAutocalculatedAbove = Cache
+ .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false);
+ viewStyle.setScaleProteinAsCdna(
+ Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true));
}
void init()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
applyViewProperties();
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
@@ -297,93 +286,54 @@ public class AlignViewport extends AlignmentViewport implements
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
+
+ showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
- String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC
+ 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);
-
- if (globalColourScheme instanceof UserColourScheme)
- {
- globalColourScheme = UserDefinedColours.loadDefaultColours();
- ((UserColourScheme) globalColourScheme).setThreshold(0,
- isIgnoreGapsConsensus());
- }
+ ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme(this,
+ alignment, schemeName);
+ residueShading = new ResidueShader(colourScheme);
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
- }
- }
-
- /**
- * get the consensus sequence as displayed under the PID consensus annotation
- * row.
- *
- * @return consensus sequence as a new sequence object
- */
- public SequenceI getConsensusSeq()
- {
- if (consensus == null)
+ if (colourScheme instanceof UserColourScheme)
{
- updateConsensus(null);
+ residueShading = new ResidueShader(
+ UserDefinedColours.loadDefaultColours());
+ residueShading.setThreshold(0, isIgnoreGapsConsensus());
}
- if (consensus == null)
- {
- return null;
- }
- StringBuffer seqs = new StringBuffer();
- for (int i = 0; i < consensus.annotations.length; i++)
+
+ if (residueShading != null)
{
- if (consensus.annotations[i] != null)
- {
- if (consensus.annotations[i].description.charAt(0) == '[')
- {
- seqs.append(consensus.annotations[i].description.charAt(1));
- }
- else
- {
- seqs.append(consensus.annotations[i].displayCharacter);
- }
- }
+ residueShading.setConsensus(hconsensus);
}
-
- SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus "
- + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
- return sq;
+ setColourAppliesToAllGroups(true);
}
boolean validCharWidth;
/**
- * update view settings with the given font. You may need to call
- * alignPanel.fontChanged to update the layout geometry
- *
- * @param setGrid
- * when true, charWidth/height is set according to font mentrics
+ * {@inheritDoc}
*/
+ @Override
public void setFont(Font f, boolean setGrid)
{
font = f;
Container c = new Container();
- java.awt.FontMetrics fm = c.getFontMetrics(font);
- int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle
- .getCharHeight();
if (setGrid)
{
+ FontMetrics fm = c.getFontMetrics(font);
+ int ww = fm.charWidth('M');
setCharHeight(fm.getHeight());
setCharWidth(ww);
}
@@ -400,7 +350,6 @@ public class AlignViewport extends AlignmentViewport implements
super.setViewStyle(settingsForView);
setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
viewStyle.getFontSize()), false);
-
}
/**
@@ -419,10 +368,11 @@ public class AlignViewport extends AlignmentViewport implements
* @param align
* DOCUMENT ME!
*/
+ @Override
public void setAlignment(AlignmentI align)
{
replaceMappings(align);
- this.alignment = align;
+ super.setAlignment(align);
}
/**
@@ -505,63 +455,6 @@ public class AlignViewport extends AlignmentViewport implements
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setCurrentTree(NJTree tree)
- {
- currentTree = tree;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public NJTree getCurrentTree()
- {
- return currentTree;
- }
-
- /**
- * returns the visible column regions of the alignment
- *
- * @param selectedRegionOnly
- * true to just return the contigs intersecting with the selected
- * area
- * @return
- */
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
- {
- int[] viscontigs = null;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes() + 1;
- }
- else
- {
- end = alignment.getWidth();
- }
- viscontigs = colSel.getVisibleContigs(start, end);
- return viscontigs;
- }
-
- /**
* get hash of undo and redo list for the alignment
*
* @return long[] { historyList.hashCode, redoList.hashCode };
@@ -625,9 +518,11 @@ public class AlignViewport extends AlignmentViewport implements
public void sendSelection()
{
jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
+ .getStructureSelectionManager(Desktop.instance)
+ .sendSelection(new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()),
+ new HiddenColumns(getAlignment().getHiddenColumns()),
+ this);
}
/**
@@ -640,8 +535,8 @@ public class AlignViewport extends AlignmentViewport implements
*/
public AlignmentPanel getAlignPanel()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
- .getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(this.getSequenceSetId());
for (int p = 0; aps != null && p < aps.length; p++)
{
if (aps[p].av == this)
@@ -672,57 +567,6 @@ public class AlignViewport extends AlignmentViewport implements
.getStructureSelectionManager(Desktop.instance);
}
- /**
- *
- * @param pdbEntries
- * @return an array of SequenceI arrays, one for each PDBEntry, listing which
- * sequences in the alignment hold a reference to it
- */
- public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
- {
- List seqvectors = new ArrayList();
- for (PDBEntry pdb : pdbEntries)
- {
- List choosenSeqs = new ArrayList();
- for (SequenceI sq : alignment.getSequences())
- {
- Vector pdbRefEntries = sq.getDatasetSequence().getAllPDBEntries();
- if (pdbRefEntries == null)
- {
- continue;
- }
- for (PDBEntry pdbRefEntry : pdbRefEntries)
- {
- if (pdbRefEntry.getId().equals(pdb.getId()))
- {
- if (pdbRefEntry.getChainCode() != null
- && pdb.getChainCode() != null)
- {
- if (pdbRefEntry.getChainCode().equalsIgnoreCase(
- pdb.getChainCode())
- && !choosenSeqs.contains(sq))
- {
- choosenSeqs.add(sq);
- continue;
- }
- }
- else
- {
- if (!choosenSeqs.contains(sq))
- {
- choosenSeqs.add(sq);
- continue;
- }
- }
-
- }
- }
- }
- seqvectors.add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
- }
- return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
- }
-
@Override
public boolean isNormaliseSequenceLogo()
{
@@ -744,7 +588,7 @@ public class AlignViewport extends AlignmentViewport implements
return validCharWidth;
}
- private Hashtable calcIdParams = new Hashtable();
+ private Hashtable calcIdParams = new Hashtable<>();
public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
@@ -760,7 +604,7 @@ public class AlignViewport extends AlignmentViewport implements
// calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
if (needsUpdate)
{
- Cache.log.debug("trigger update for " + calcId);
+ Console.debug("trigger update for " + calcId);
}
}
@@ -774,7 +618,8 @@ public class AlignViewport extends AlignmentViewport implements
*
* - compute the equivalent edit on the mapped sequences
* - apply the mapped edit
- * - 'apply' the source edit to the working copy of the source sequences
+ * - 'apply' the source edit to the working copy of the source
+ * sequences
*
*
* @param command
@@ -849,16 +694,20 @@ public class AlignViewport extends AlignmentViewport implements
{
if (AlignmentUtils.isMappable(toAdd, getAlignment()))
{
- if (openLinkedAlignment(toAdd, title))
- {
- return;
- }
+ openLinkedAlignment(toAdd, title);
+ return;
}
}
+ addDataToAlignment(toAdd);
+ }
- /*
- * No mappings, or offer declined - add sequences to this alignment
- */
+ /**
+ * adds sequences to this alignment
+ *
+ * @param toAdd
+ */
+ void addDataToAlignment(AlignmentI toAdd)
+ {
// TODO: JAL-407 regardless of above - identical sequences (based on ID and
// provenance) should share the same dataset sequence
@@ -879,12 +728,62 @@ public class AlignViewport extends AlignmentViewport implements
al.addSequence(seq);
}
}
-
- setEndSeq(getAlignment().getHeight());
+ for (ContactMatrixI cm : toAdd.getContactMaps())
+ {
+ al.addContactList(cm);
+ }
+ ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
firePropertyChange("alignment", null, getAlignment().getSequences());
}
/**
+ * Load a File into this AlignViewport attempting to detect format if not
+ * given or given as null.
+ *
+ * @param file
+ * @param format
+ */
+ public void addFile(File file, FileFormatI format)
+ {
+ addFile(file, format, true);
+ }
+
+ public void addFile(File file, FileFormatI format, boolean async)
+ {
+ DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
+
+ if (format == null)
+ {
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e1)
+ {
+ jalview.bin.Console.error("Unknown file format for '" + file + "'");
+ }
+ }
+ else if (FileFormats.getInstance().isIdentifiable(format))
+ {
+ try
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ } catch (FileFormatException e)
+ {
+ jalview.bin.Console.error("Unknown file format for '" + file + "'",
+ e);
+ }
+ }
+
+ new FileLoader().LoadFile(this, file, DataSourceType.FILE, format,
+ async);
+ }
+
+ public void addFile(File file)
+ {
+ addFile(file, null);
+ }
+
+ /**
* Show a dialog with the option to open and link (cDNA <-> protein) as a new
* alignment, either as a standalone alignment or in a split frame. Returns
* true if the new alignment was opened, false if not, because the user
@@ -893,31 +792,43 @@ public class AlignViewport extends AlignmentViewport implements
* @param al
* @param title
*/
- protected boolean openLinkedAlignment(AlignmentI al, String title)
+ protected void openLinkedAlignment(AlignmentI al, String title)
{
- String[] options = new String[] {
- MessageManager.getString("action.no"),
+ String[] options = new String[] { MessageManager.getString("action.no"),
MessageManager.getString("label.split_window"),
MessageManager.getString("label.new_window"), };
final String question = JvSwingUtils.wrapTooltip(true,
MessageManager.getString("label.open_split_window?"));
- int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ final AlignViewport us = this;
+
+ /*
+ * options No, Split Window, New Window correspond to
+ * dialog responses 0, 1, 2 (even though JOptionPane shows them
+ * in reverse order)
+ */
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
+ .setResponseHandler(0, () -> {
+ addDataToAlignment(al);
+ }).setResponseHandler(1, () -> {
+ us.openLinkedAlignmentAs(al, title, true);
+ }).setResponseHandler(2, () -> {
+ us.openLinkedAlignmentAs(al, title, false);
+ });
+ dialog.showDialog(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)
- {
- return false;
- }
- final boolean openSplitPane = (response == 1);
- final boolean openInNewWindow = (response == 2);
-
+ protected void openLinkedAlignmentAs(AlignmentI al, String title,
+ boolean newWindowOrSplitPane)
+ {
/*
* Identify protein and dna alignments. Make a copy of this one if opening
* in a new split pane.
*/
- AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ AlignmentI thisAlignment = newWindowOrSplitPane
+ ? new Alignment(getAlignment())
: getAlignment();
AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
@@ -938,17 +849,18 @@ public class AlignViewport extends AlignmentViewport implements
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
- newAlignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file", new Object[] { title }));
+ newAlignFrame.setStatus(MessageManager
+ .formatMessage("label.successfully_loaded_file", new Object[]
+ { title }));
// 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);
// }
- if (openInNewWindow)
+ if (!newWindowOrSplitPane)
{
Desktop.addInternalFrame(newAlignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -956,19 +868,16 @@ public class AlignViewport extends AlignmentViewport implements
try
{
- newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
+ newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
- if (openSplitPane)
+ if (newWindowOrSplitPane)
{
al.alignAs(thisAlignment);
protein = openSplitFrame(newAlignFrame, thisAlignment);
}
-
- return true;
}
/**
@@ -989,8 +898,8 @@ public class AlignViewport extends AlignmentViewport implements
* is protein, the mappings to cDNA will be registered with
* StructureSelectionManager as a side-effect.
*/
- AlignFrame copyMe = new AlignFrame(complement,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
AlignmentI al = newAlignFrame.viewport.getAlignment();
@@ -1030,10 +939,9 @@ public class AlignViewport extends AlignmentViewport implements
if (ap != null)
{
// modify GUI elements to reflect geometry change
- Dimension idw = getAlignPanel().getIdPanel().getIdCanvas()
- .getPreferredSize();
+ Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
idw.width = i;
- getAlignPanel().getIdPanel().getIdCanvas().setPreferredSize(idw);
+ ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
}
}
@@ -1068,15 +976,16 @@ 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.setDontScrollComplement(true);
+ complementPanel.setToScrollComplementPanel(false);
complementPanel.scrollToCentre(sr, verticalOffset);
+ complementPanel.setToScrollComplementPanel(true);
}
}
@@ -1088,7 +997,7 @@ public class AlignViewport extends AlignmentViewport implements
*/
protected boolean noReferencesTo(AlignedCodonFrame acf)
{
- AlignFrame[] frames = Desktop.getAlignFrames();
+ AlignFrame[] frames = Desktop.getDesktopAlignFrames();
if (frames == null)
{
return true;
@@ -1121,6 +1030,35 @@ public class AlignViewport extends AlignmentViewport implements
@Override
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
{
+ transferFeaturesStyles(featureSettings, false);
+ }
+
+ /**
+ * 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 mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
+ {
+ transferFeaturesStyles(featureSettings, true);
+ }
+
+ /**
+ * when mergeOnly is set, then group and feature visibility or feature colours
+ * are not modified for features and groups already known to the feature
+ * renderer. Feature ordering is always adjusted, and transparency is always
+ * set regardless.
+ *
+ * @param featureSettings
+ * @param mergeOnly
+ */
+ private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
+ boolean mergeOnly)
+ {
if (featureSettings == null)
{
return;
@@ -1128,12 +1066,25 @@ public class AlignViewport extends AlignmentViewport implements
FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
.getFeatureRenderer();
+ List origRenderOrder = new ArrayList<>();
+ List origGroups = new ArrayList<>();
+ // preserve original render order - allows differentiation between user
+ // configured colours and autogenerated ones
+ origRenderOrder.addAll(fr.getRenderOrder());
+ origGroups.addAll(fr.getFeatureGroups());
+
fr.findAllFeatures(true);
List renderOrder = fr.getRenderOrder();
FeaturesDisplayedI displayed = fr.getFeaturesDisplayed();
- displayed.clear();
+ if (!mergeOnly)
+ {
+ // only clear displayed features if we are mergeing
+ // displayed.clear();
+ }
// TODO this clears displayed.featuresRegistered - do we care?
-
+ //
+ // JAL-3330 - JBP - yes we do - calling applyFeatureStyle to a view where
+ // feature visibility has already been configured is not very friendly
/*
* set feature colour if specified by feature settings
* set visibility of all features
@@ -1142,13 +1093,29 @@ public class AlignViewport extends AlignmentViewport implements
{
FeatureColourI preferredColour = featureSettings
.getFeatureColour(type);
- if (preferredColour != null)
- {
- fr.setColour(type, preferredColour);
- }
- if (featureSettings.isFeatureDisplayed(type))
+ FeatureColourI origColour = fr.getFeatureStyle(type);
+ if (!mergeOnly || (!origRenderOrder.contains(type)
+ || origColour == null
+ || (!origColour.isGraduatedColour()
+ && origColour.getColour() != null
+ && origColour.getColour().equals(
+ ColorUtils.createColourFromName(type)))))
{
- displayed.setVisible(type);
+ // if we are merging, only update if there wasn't already a colour
+ // defined for
+ // this type
+ if (preferredColour != null)
+ {
+ fr.setColour(type, preferredColour);
+ }
+ if (featureSettings.isFeatureDisplayed(type))
+ {
+ displayed.setVisible(type);
+ }
+ else if (featureSettings.isFeatureHidden(type))
+ {
+ displayed.setHidden(type);
+ }
}
}
@@ -1157,7 +1124,13 @@ public class AlignViewport extends AlignmentViewport implements
*/
for (String group : fr.getFeatureGroups())
{
- fr.setGroupVisibility(group, featureSettings.isGroupDisplayed(group));
+ if (!mergeOnly || !origGroups.contains(group))
+ {
+ // when merging, display groups only if the aren't already marked as not
+ // visible
+ fr.setGroupVisibility(group,
+ featureSettings.isGroupDisplayed(group));
+ }
}
/*
@@ -1172,6 +1145,18 @@ public class AlignViewport extends AlignmentViewport implements
fr.orderFeatures(featureSettings);
}
fr.setTransparency(featureSettings.getTransparency());
+
+ fr.notifyFeaturesChanged();
+ }
+
+ public String getViewName()
+ {
+ return viewName;
+ }
+
+ public void setViewName(String viewName)
+ {
+ this.viewName = viewName;
}
}