X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=9aac56da14e7742c5e50bed5f60c3461974df9c2;hb=6200addf078b7f7ace90597dc056dafc7fc602c1;hp=1a328f9a936cd4b85cdb7928fa21195ca10aff54;hpb=227ee1c1c69c228b67d408a0a83ae51bf5811272;p=jalview.git
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 1a328f9..954cfcc 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 2.8.2)
- * Copyright (C) 2014 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.
*
@@ -18,53 +18,51 @@
* 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.NJTree;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
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.datamodel.AlignmentAnnotation;
+import jalview.commands.CommandI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.Sequence;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
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.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.Color;
import java.awt.Container;
+import java.awt.Dimension;
import java.awt.Font;
+import java.awt.FontMetrics;
import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.Hashtable;
-import java.util.Stack;
-import java.util.Vector;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
/**
* DOCUMENT ME!
@@ -72,82 +70,29 @@ import java.util.Vector;
* @author $author$
* @version $Revision: 1.141 $
*/
-public class AlignViewport extends AlignmentViewport implements
- SelectionSource, VamsasSource, AlignViewportI
+public class AlignViewport extends AlignmentViewport
+ implements SelectionSource
{
- int startRes;
-
- int endRes;
-
- int startSeq;
-
- int endSeq;
-
- boolean showJVSuffix = true;
-
- boolean showText = true;
-
- boolean showColourText = false;
-
- boolean showBoxes = true;
-
- boolean wrapAlignment = false;
-
- boolean renderGaps = true;
-
- boolean showSequenceFeatures = false;
-
- boolean showAnnotation = true;
-
- int charHeight;
-
- int charWidth;
-
- boolean validCharWidth;
-
- int wrappedWidth;
-
Font font;
- boolean seqNameItalics;
-
- NJTree currentTree = null;
-
- boolean scaleAboveWrapped = false;
-
- boolean scaleLeftWrapped = true;
-
- boolean scaleRightWrapped = true;
-
- boolean showHiddenMarkers = true;
-
boolean cursorMode = false;
- /**
- * Keys are the feature types which are currently visible. Note: Values are
- * not used!
- */
- private Hashtable featuresDisplayed = null;
-
boolean antiAlias = false;
- Rectangle explodedPosition;
-
- String viewName;
+ private Rectangle explodedGeometry = null;
- boolean gatherViewsHere = false;
+ private String viewName = null;
- Stack historyList = new Stack();
-
- Stack redoList = new Stack();
-
- int thresholdTextColour = 0;
-
- Color textColour = Color.black;
-
- Color textColour2 = Color.white;
+ /*
+ * Flag set true on the view that should 'gather' multiple views of the same
+ * sequence set id when a project is reloaded. Set false on all views when
+ * they are 'exploded' into separate windows. Set true on the current view
+ * when 'Gather' is performed, and also on the first tab when the first new
+ * view is created.
+ */
+ private boolean gatherViewsHere = false;
- boolean rightAlignIds = false;
+ private AnnotationColumnChooser annotationColumnSelectionState;
/**
* Creates a new AlignViewport object.
@@ -157,7 +102,7 @@ public class AlignViewport extends AlignmentViewport implements
*/
public AlignViewport(AlignmentI al)
{
- setAlignment(al);
+ super(al);
init();
}
@@ -175,20 +120,21 @@ 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)
{
- Cache.log.debug("Setting viewport's sequence set id : "
- + sequenceSetID);
+ Cache.log.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
init();
+
}
/**
@@ -199,21 +145,12 @@ 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)
{
- this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null
- && hiddenColumns.getHiddenColumns().size() > 0)
- {
- hasHiddenColumns = true;
- }
- else
- {
- hasHiddenColumns = false;
- }
+ al.setHiddenColumns(hiddenColumns);
}
init();
}
@@ -226,7 +163,7 @@ 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);
@@ -242,63 +179,75 @@ 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)
{
- Cache.log.debug("Setting viewport's sequence set id : "
- + sequenceSetID);
+ Cache.log.debug(
+ "Setting viewport's sequence set id : " + sequenceSetID);
}
if (Cache.log != null && Cache.log.isDebugEnabled() && viewId != null)
{
Cache.log.debug("Setting viewport's view id : " + viewId);
}
- setAlignment(al);
+
if (hiddenColumns != null)
{
- this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null
- && hiddenColumns.getHiddenColumns().size() > 0)
- {
- hasHiddenColumns = true;
- }
- else
- {
- hasHiddenColumns = false;
- }
+ al.setHiddenColumns(hiddenColumns);
}
init();
}
- void init()
+ /**
+ * Apply any settings saved in user preferences
+ */
+ private void applyViewProperties()
{
- this.startRes = 0;
- this.endRes = alignment.getWidth() - 1;
- this.startSeq = 0;
- this.endSeq = alignment.getHeight() - 1;
+ // BH! using final static strings here because we also use these in
+ // JS version startup api
+ // BH was false
+ antiAlias = Cache.getDefault(Preferences.ANTI_ALIAS, true);
- antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+ viewStyle.setShowJVSuffix(
+ Cache.getDefault(Preferences.SHOW_JVSUFFIX, true));
+ setShowAnnotation(Cache.getDefault(Preferences.SHOW_ANNOTATIONS, true));
- showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
- showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+ setRightAlignIds(Cache.getDefault(Preferences.RIGHT_ALIGN_IDS, false));
+ setCentreColumnLabels(Cache.getDefault(Preferences.CENTRE_COLUMN_LABELS, false));
+ autoCalculateConsensusAndConservation = Cache.getDefault(Preferences.AUTO_CALC_CONSENSUS, true);
- rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
- centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
- autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
-
- setPadGaps(Cache.getDefault("PAD_GAPS", true));
- shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
- showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
+ setPadGaps(Cache.getDefault(Preferences.PAD_GAPS, true));
+ setShowNPFeats(Cache.getDefault(Preferences.SHOW_NPFEATS_TOOLTIP, true));
+ setShowDBRefs(Cache.getDefault(Preferences.SHOW_DBREFS_TOOLTIP, true));
+ viewStyle.setSeqNameItalics(Cache.getDefault(Preferences.ID_ITALICS, true));
+ viewStyle.setWrapAlignment(
+ Cache.getDefault(Preferences.WRAP_ALIGNMENT, false));
+ viewStyle.setShowUnconserved(
+ Cache.getDefault(Preferences.SHOW_UNCONSERVED, false));
+ sortByTree = Cache.getDefault(Preferences.SORT_BY_TREE, false);
+ followSelection = Cache.getDefault(Preferences.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));
+ }
- String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
- String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
- String fontSize = Cache.getDefault("FONT_SIZE", "10");
+ void init()
+ {
+ applyViewProperties();
- seqNameItalics = Cache.getDefault("ID_ITALICS", true);
+ String fontName = Cache.getDefault(Preferences.FONT_NAME, "SansSerif");
+ String fontStyle = Cache.getDefault(Preferences.FONT_STYLE,
+ Font.PLAIN + "");
+ String fontSize = Cache.getDefault(Preferences.FONT_SIZE, "10");
int style = 0;
@@ -311,10 +260,11 @@ public class AlignViewport extends AlignmentViewport implements
style = 2;
}
- setFont(new Font(fontName, style, Integer.parseInt(fontSize)));
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
alignment
- .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
+ .setGapCharacter(Cache.getDefault(Preferences.GAP_SYMBOL, "-")
+ .charAt(0));
// We must set conservation and consensus before setting colour,
// as Blosum and Clustal require this to be done
@@ -322,124 +272,86 @@ public class AlignViewport extends AlignmentViewport implements
{
if (!alignment.isNucleotide())
{
- showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
- showQuality = Cache.getDefault("SHOW_QUALITY", true);
- showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
- false);
+ showConservation = Cache.getDefault(Preferences.SHOW_CONSERVATION,
+ true);
+ showQuality = Cache.getDefault(Preferences.SHOW_QUALITY, true);
+ showGroupConservation = Cache
+ .getDefault(Preferences.SHOW_GROUP_CONSERVATION, false);
}
- showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
- true);
- showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
- normaliseSequenceLogo = Cache.getDefault("NORMALISE_CONSENSUS_LOGO",
+ showConsensusHistogram = Cache
+ .getDefault(Preferences.SHOW_CONSENSUS_HISTOGRAM, true);
+ showSequenceLogo = Cache.getDefault(Preferences.SHOW_CONSENSUS_LOGO,
false);
- showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
- showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
+
+ normaliseSequenceLogo = Cache
+ .getDefault(Preferences.NORMALISE_CONSENSUS_LOGO, false);
+ showGroupConsensus = Cache
+ .getDefault(Preferences.SHOW_GROUP_CONSENSUS, false);
+ showConsensus = Cache.getDefault(Preferences.SHOW_IDENTITY, true);
+
+ showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true);
}
initAutoAnnotation();
- if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
+ String colourProperty = alignment.isNucleotide()
+ ? Preferences.DEFAULT_COLOUR_NUC
+ : Preferences.DEFAULT_COLOUR_PROT;
+ String schemeName = Cache.getProperty(colourProperty);
+ if (schemeName == null)
{
- globalColourScheme = ColourSchemeProperty.getColour(alignment,
- jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));
-
- if (globalColourScheme instanceof UserColourScheme)
- {
- globalColourScheme = UserDefinedColours.loadDefaultColours();
- ((UserColourScheme) globalColourScheme).setThreshold(0,
- getIgnoreGapsConsensus());
- }
-
- if (globalColourScheme != null)
- {
- globalColourScheme.setConsensus(hconsensus);
- }
+ // only DEFAULT_COLOUR available in Jalview before 2.9
+ schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
}
+ ColourSchemeI colourScheme = ColourSchemeProperty
+ .getColourScheme(this, alignment, schemeName);
+ residueShading = new ResidueShader(colourScheme);
- wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED",
- false);
- sortByTree = jalview.bin.Cache.getDefault("SORT_BY_TREE", false);
- followSelection = jalview.bin.Cache.getDefault("FOLLOW_SELECTIONS",
- true);
- }
+ if (colourScheme instanceof UserColourScheme)
+ {
+ residueShading = new ResidueShader(
+ UserDefinedColours.loadDefaultColours());
+ residueShading.setThreshold(0, isIgnoreGapsConsensus());
+ }
- /**
- * set the flag
- *
- * @param b
- * features are displayed if true
- */
- public void setShowSequenceFeatures(boolean b)
- {
- showSequenceFeatures = b;
+ if (residueShading != null)
+ {
+ residueShading.setConsensus(hconsensus);
+ }
+ setColourAppliesToAllGroups(true);
}
- public boolean getShowSequenceFeatures()
- {
- return showSequenceFeatures;
- }
+ boolean validCharWidth;
/**
- * centre columnar annotation labels in displayed alignment annotation TODO:
- * add to jalviewXML and annotation display settings
+ * {@inheritDoc}
*/
- boolean centreColumnLabels = false;
-
- private boolean showdbrefs;
-
- private boolean shownpfeats;
+ @Override
+ public void setFont(Font f, boolean setGrid)
+ {
+ font = f;
- // --------END Structure Conservation
+ Container c = new Container();
- /**
- * 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)
- {
- updateConsensus(null);
- }
- if (consensus == null)
- {
- return null;
- }
- StringBuffer seqs = new StringBuffer();
- for (int i = 0; i < consensus.annotations.length; i++)
+ if (setGrid)
{
- 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);
- }
- }
+ FontMetrics fm = c.getFontMetrics(font);
+ int ww = fm.charWidth('M');
+ setCharHeight(fm.getHeight());
+ setCharWidth(ww);
}
+ viewStyle.setFontName(font.getName());
+ viewStyle.setFontStyle(font.getStyle());
+ viewStyle.setFontSize(font.getSize());
- SequenceI sq = new Sequence("Consensus", seqs.toString());
- sq.setDescription("Percentage Identity Consensus "
- + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));
- return sq;
+ validCharWidth = true;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getStartRes()
+ @Override
+ public void setViewStyle(ViewStyleI settingsForView)
{
- return startRes;
+ super.setViewStyle(settingsForView);
+ setFont(new Font(viewStyle.getFontName(), viewStyle.getFontStyle(),
+ viewStyle.getFontSize()), false);
}
/**
@@ -447,831 +359,796 @@ public class AlignViewport extends AlignmentViewport implements
*
* @return DOCUMENT ME!
*/
- public int getEndRes()
+ public Font getFont()
{
- return endRes;
+ return font;
}
/**
* DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @param align
+ * DOCUMENT ME!
*/
- public int getStartSeq()
+ @Override
+ public void setAlignment(AlignmentI align)
{
- return startSeq;
+ replaceMappings(align);
+ super.setAlignment(align);
}
/**
- * DOCUMENT ME!
+ * Replace any codon mappings for this viewport with those for the given
+ * viewport
*
- * @param res
- * DOCUMENT ME!
+ * @param align
*/
- public void setStartRes(int res)
+ public void replaceMappings(AlignmentI align)
+ {
+
+ /*
+ * Deregister current mappings (if any)
+ */
+ deregisterMappings();
+
+ /*
+ * Register new mappings (if any)
+ */
+ if (align != null)
+ {
+ Desktop.getStructureSelectionManager()
+ .registerMappings(align.getCodonFrames());
+ }
+
+ /*
+ * replace mappings on our alignment
+ */
+ if (alignment != null && align != null)
+ {
+ alignment.setCodonFrames(align.getCodonFrames());
+ }
+ }
+
+ protected void deregisterMappings()
{
- this.startRes = res;
+ AlignmentI al = getAlignment();
+ if (al != null)
+ {
+ List mappings = al.getCodonFrames();
+ if (mappings != null)
+ {
+ StructureSelectionManager ssm = Desktop
+ .getStructureSelectionManager();
+ for (AlignedCodonFrame acf : mappings)
+ {
+ if (noReferencesTo(acf))
+ {
+ ssm.deregisterMapping(acf);
+ }
+ }
+ }
+ }
}
/**
* DOCUMENT ME!
*
- * @param seq
- * DOCUMENT ME!
+ * @return DOCUMENT ME!
*/
- public void setStartSeq(int seq)
+ @Override
+ public char getGapCharacter()
{
- this.startSeq = seq;
+ return getAlignment().getGapCharacter();
}
/**
* DOCUMENT ME!
*
- * @param res
+ * @param gap
* DOCUMENT ME!
*/
- public void setEndRes(int res)
+ public void setGapCharacter(char gap)
{
- if (res > (alignment.getWidth() - 1))
- {
- // log.System.out.println(" Corrected res from " + res + " to maximum " +
- // (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
- }
-
- if (res < 0)
+ if (getAlignment() != null)
{
- res = 0;
+ getAlignment().setGapCharacter(gap);
}
-
- this.endRes = res;
}
/**
- * DOCUMENT ME!
+ * returns the visible column regions of the alignment
*
- * @param seq
- * DOCUMENT ME!
+ * @param selectedRegionOnly
+ * true to just return the contigs intersecting with the selected
+ * area
+ * @return
*/
- public void setEndSeq(int seq)
+ public Iterator getViewAsVisibleContigs(boolean selectedRegionOnly)
{
- if (seq > alignment.getHeight())
+ int start = 0;
+ int end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
{
- seq = alignment.getHeight();
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
}
-
- if (seq < 0)
+ else
{
- seq = 0;
+ end = alignment.getWidth();
}
-
- this.endSeq = seq;
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
}
/**
- * DOCUMENT ME!
+ * get hash of undo and redo list for the alignment
*
- * @return DOCUMENT ME!
+ * @return long[] { historyList.hashCode, redoList.hashCode };
*/
- public int getEndSeq()
+ public long[] getUndoRedoHash()
{
- return endSeq;
+ // TODO: JAL-1126
+ if (historyList == null || redoList == null)
+ {
+ return new long[] { -1, -1 };
+ }
+ return new long[] { historyList.hashCode(), this.redoList.hashCode() };
}
/**
- * DOCUMENT ME!
+ * test if a particular set of hashcodes are different to the hashcodes for
+ * the undo and redo list.
*
- * @param f
- * DOCUMENT ME!
+ * @param undoredo
+ * the stored set of hashcodes as returned by getUndoRedoHash
+ * @return true if the hashcodes differ (ie the alignment has been edited) or
+ * the stored hashcode array differs in size
*/
- public void setFont(Font f)
+ public boolean isUndoRedoHashModified(long[] undoredo)
{
- font = f;
-
- Container c = new Container();
+ if (undoredo == null)
+ {
+ return true;
+ }
+ long[] cstate = getUndoRedoHash();
+ if (cstate.length != undoredo.length)
+ {
+ return true;
+ }
- java.awt.FontMetrics fm = c.getFontMetrics(font);
- setCharHeight(fm.getHeight());
- setCharWidth(fm.charWidth('M'));
- validCharWidth = true;
+ for (int i = 0; i < cstate.length; i++)
+ {
+ if (cstate[i] != undoredo[i])
+ {
+ return true;
+ }
+ }
+ return false;
}
+ public boolean followSelection = true;
+
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
*/
- public Font getFont()
+ public boolean getFollowSelection()
{
- return font;
+ return followSelection;
}
/**
- * DOCUMENT ME!
- *
- * @param w
- * DOCUMENT ME!
+ * Send the current selection to be broadcast to any selection listeners.
*/
- public void setCharWidth(int w)
+ @Override
+ public void sendSelection()
{
- this.charWidth = w;
+ Desktop.getStructureSelectionManager().sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()),
+ new HiddenColumns(getAlignment().getHiddenColumns()), this);
}
/**
- * DOCUMENT ME!
+ * return the alignPanel containing the given viewport. Use this to get the
+ * components currently handling the given viewport.
*
- * @return DOCUMENT ME!
+ * @param av
+ * @return null or an alignPanel guaranteed to have non-null alignFrame
+ * reference
*/
- public int getCharWidth()
+ public AlignmentPanel getAlignPanel()
{
- return charWidth;
+ AlignmentPanel[] aps = PaintRefresher
+ .getAssociatedPanels(this.getSequenceSetId());
+ for (int p = 0; aps != null && p < aps.length; p++)
+ {
+ if (aps[p].av == this)
+ {
+ return aps[p];
+ }
+ }
+ return null;
}
- /**
- * DOCUMENT ME!
- *
- * @param h
- * DOCUMENT ME!
- */
- public void setCharHeight(int h)
+ public boolean getSortByTree()
{
- this.charHeight = h;
+ return sortByTree;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getCharHeight()
+ public void setSortByTree(boolean sort)
{
- return charHeight;
+ sortByTree = sort;
}
/**
- * DOCUMENT ME!
- *
- * @param w
- * DOCUMENT ME!
+ * Returns the (Desktop) instance of the StructureSelectionManager
*/
- public void setWrappedWidth(int w)
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
{
- this.wrappedWidth = w;
+ return Desktop.getStructureSelectionManager();
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWrappedWidth()
+ @Override
+ public boolean isNormaliseSequenceLogo()
{
- return wrappedWidth;
+ return normaliseSequenceLogo;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public AlignmentI getAlignment()
+ public void setNormaliseSequenceLogo(boolean state)
{
- return alignment;
+ normaliseSequenceLogo = state;
}
/**
- * DOCUMENT ME!
*
- * @param align
- * DOCUMENT ME!
- */
- public void setAlignment(AlignmentI align)
- {
- if (alignment != null && alignment.getCodonFrames() != null)
- {
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).removeMappings(alignment.getCodonFrames());
- }
- this.alignment = align;
- if (alignment != null && alignment.getCodonFrames() != null)
- {
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).addMappings(alignment.getCodonFrames());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setWrapAlignment(boolean state)
- {
- wrapAlignment = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowText(boolean state)
- {
- showText = state;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
+ * @return true if alignment characters should be displayed
*/
- public void setRenderGaps(boolean state)
+ @Override
+ public boolean isValidCharWidth()
{
- renderGaps = state;
+ return validCharWidth;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourText()
- {
- return showColourText;
- }
+ private Hashtable calcIdParams = new Hashtable<>();
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setColourText(boolean state)
+ public AutoCalcSetting getCalcIdSettingsFor(String calcId)
{
- showColourText = state;
+ return calcIdParams.get(calcId);
}
- /**
- * DOCUMENT ME!
- *
- * @param state
- * DOCUMENT ME!
- */
- public void setShowBoxes(boolean state)
+ public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
+ boolean needsUpdate)
{
- showBoxes = state;
+ calcIdParams.put(calcId, settings);
+ // TODO: create a restart list to trigger any calculations that need to be
+ // restarted after load
+ // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
+ if (needsUpdate)
+ {
+ Cache.log.debug("trigger update for " + calcId);
+ }
}
/**
- * DOCUMENT ME!
+ * Method called when another alignment's edit (or possibly other) command is
+ * broadcast to here.
+ *
+ * To allow for sequence mappings (e.g. protein to cDNA), we have to first
+ * 'unwind' the command on the source sequences (in simulation, not in fact),
+ * and then for each edit in turn:
+ *
+ * - compute the equivalent edit on the mapped sequences
+ * - apply the mapped edit
+ * - 'apply' the source edit to the working copy of the source
+ * sequences
+ *
*
- * @return DOCUMENT ME!
- */
- public boolean getWrapAlignment()
- {
- return wrapAlignment;
- }
+ * @param command
+ * @param undo
+ * @param ssm
+ */
+ @Override
+ public void mirrorCommand(CommandI command, boolean undo,
+ StructureSelectionManager ssm, VamsasSource source)
+ {
+ /*
+ * Do nothing unless we are a 'complement' of the source. May replace this
+ * with direct calls not via SSM.
+ */
+ if (source instanceof AlignViewportI
+ && ((AlignViewportI) source).getCodingComplement() == this)
+ {
+ // ok to continue;
+ }
+ else
+ {
+ return;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowText()
- {
- return showText;
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
+ getGapCharacter());
+ if (mappedCommand != null)
+ {
+ AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
+ mappedCommand.doCommand(views);
+ getAlignPanel().alignmentChanged();
+ }
}
/**
- * DOCUMENT ME!
+ * Add the sequences from the given alignment to this viewport. Optionally,
+ * may give the user the option to open a new frame, or split panel, with cDNA
+ * and protein linked.
*
- * @return DOCUMENT ME!
- */
- public boolean getShowBoxes()
- {
- return showBoxes;
+ * @param toAdd
+ * @param title
+ */
+ public void addAlignment(AlignmentI toAdd, String title)
+ {
+ // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
+
+ // JBPComment: title is a largely redundant parameter at the moment
+ // JBPComment: this really should be an 'insert/pre/append' controller
+ // JBPComment: but the DNA/Protein check makes it a bit more complex
+
+ // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
+ // this comment:
+ // TODO: create undo object for this JAL-1101
+
+ /*
+ * 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 (AlignmentUtils.isMappable(toAdd, getAlignment()))
+ {
+ openLinkedAlignment(toAdd, title);
+ return;
+ }
+ }
+ addDataToAlignment(toAdd);
}
/**
- * DOCUMENT ME!
+ * adds sequences to this alignment
*
- * @return DOCUMENT ME!
+ * @param toAdd
*/
- public char getGapCharacter()
+ void addDataToAlignment(AlignmentI toAdd)
{
- return getAlignment().getGapCharacter();
- }
+ // TODO: JAL-407 regardless of above - identical sequences (based on ID and
+ // provenance) should share the same dataset sequence
- /**
- * DOCUMENT ME!
- *
- * @param gap
- * DOCUMENT ME!
- */
- public void setGapCharacter(char gap)
- {
- if (getAlignment() != null)
+ AlignmentI al = getAlignment();
+ String gap = String.valueOf(al.getGapCharacter());
+ for (int i = 0; i < toAdd.getHeight(); i++)
{
- getAlignment().setGapCharacter(gap);
+ 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);
+ }
}
- }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public ColumnSelection getColumnSelection()
- {
- return colSel;
+ ranges.setEndSeq(getAlignment().getHeight() - 1); // BH 2019.04.18
+ firePropertyChange("alignment", null, getAlignment().getSequences());
}
- /**
- * DOCUMENT ME!
- *
- * @param tree
- * DOCUMENT ME!
- */
- public void setCurrentTree(NJTree tree)
- {
- currentTree = tree;
- }
+ public final static int NO_SPLIT = 0;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public NJTree getCurrentTree()
- {
- return currentTree;
- }
+ public final static int SPLIT_FRAME = 1;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
+ public final static int NEW_WINDOW = 2;
/**
- * DOCUMENT ME!
+ * 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
+ * declined the offer.
*
- * @param b
- * DOCUMENT ME!
- */
- public void setShowJVSuffix(boolean b)
- {
- showJVSuffix = b;
- }
-
- /**
- * DOCUMENT ME!
+ * @param al
+ * @param title
+ */
+ protected void openLinkedAlignment(AlignmentI al, String title)
+ {
+ 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?"));
+
+ /*
+ * 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.getDesktopPane())
+ .setResponseHandler(NO_SPLIT, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ addDataToAlignment(al);
+ }
+ }).setResponseHandler(SPLIT_FRAME, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ openLinkedAlignmentAs(getAlignPanel().alignFrame,
+ new Alignment(getAlignment()), al, title,
+ SPLIT_FRAME);
+ }
+ }).setResponseHandler(NEW_WINDOW, new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ openLinkedAlignmentAs(null, getAlignment(), al, title,
+ NEW_WINDOW);
+ }
+ });
+ dialog.showDialog(question,
+ MessageManager.getString("label.open_split_window"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ }
+
+ /**
+ * Open a split frame or a new window
*
- * @return DOCUMENT ME!
- */
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
+ * @param al
+ * @param title
+ * @param mode
+ * SPLIT_FRAME or NEW_WINDOW
+ */
+ public static void openLinkedAlignmentAs(AlignFrame thisFrame,
+ AlignmentI thisAlignment, AlignmentI al, String title, int mode)
+ {
+ // BH: thisAlignment is already a copy if mode == SPLIT_FRAME
+ // Identify protein and dna alignments. Make a copy of this one if opening
+ // in a new split pane.
+
+ AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+ /*
+ * Map sequences. At least one should get mapped as we have already passed
+ * the test for 'mappability'. Any mappings made will be added to the
+ * protein alignment. Note creating dataset sequences on the new alignment
+ * is a pre-requisite for building mappings.
+ */
+ al.setDataset(null);
+ AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
+
+ /*
+ * Create the AlignFrame for the added alignment. If it is protein, mappings
+ * are registered with StructureSelectionManager as a side-effect.
+ */
+ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ newAlignFrame.setTitle(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(DataSourceType.PASTE))
+ // {
+ // alignFrame.setFileName(file, format);
+ // }
+
+ if (mode == NEW_WINDOW)
+ {
+ Desktop.addInternalFrame(newAlignFrame, title,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
+ try
+ {
+ newAlignFrame.setMaximum(Cache.getDefault(Preferences.SHOW_FULLSCREEN, false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
+ if (mode == SPLIT_FRAME)
+ {
+ al.alignAs(thisAlignment);
+ openSplitFrame(thisFrame, newAlignFrame, thisAlignment);
+ }
}
/**
- * DOCUMENT ME!
+ * Helper method to open a new SplitFrame holding linked dna and protein
+ * alignments.
*
- * @return DOCUMENT ME!
+ * @param newAlignFrame
+ * containing a new alignment to be shown
+ * @param complement
+ * cdna/protein complement alignment to show in the other split half
+ * @return the protein alignment in the split frame
*/
- public boolean getScaleLeftWrapped()
+ static protected AlignmentI openSplitFrame(AlignFrame thisFrame,
+ AlignFrame newAlignFrame, AlignmentI complement)
{
- return scaleLeftWrapped;
- }
+ /*
+ * Make a new frame with a copy of the alignment we are adding to. If this
+ * 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);
+ copyMe.setTitle(thisFrame.getTitle());
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
+ AlignmentI al = newAlignFrame.viewport.getAlignment();
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+
+ return proteinFrame.viewport.getAlignment();
}
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleAboveWrapped(boolean b)
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
{
- scaleAboveWrapped = b;
+ return annotationColumnSelectionState;
}
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleLeftWrapped(boolean b)
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser currentAnnotationColumnSelectionState)
{
- scaleLeftWrapped = b;
+ this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
}
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setScaleRightWrapped(boolean b)
+ @Override
+ public void setIdWidth(int i)
{
- scaleRightWrapped = b;
+ super.setIdWidth(i);
+ AlignmentPanel ap = getAlignPanel();
+ if (ap != null)
+ {
+ // modify GUI elements to reflect geometry change
+ Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
+ idw.width = i;
+ ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
+ }
}
- public void setDataset(boolean b)
+ public Rectangle getExplodedGeometry()
{
- isDataset = b;
+ return explodedGeometry;
}
- public boolean isDataset()
+ public void setExplodedGeometry(Rectangle explodedPosition)
{
- return isDataset;
+ this.explodedGeometry = explodedPosition;
}
- public boolean getShowHiddenMarkers()
+ public boolean isGatherViewsHere()
{
- return showHiddenMarkers;
+ return gatherViewsHere;
}
- public void setShowHiddenMarkers(boolean show)
+ public void setGatherViewsHere(boolean gatherViewsHere)
{
- showHiddenMarkers = show;
+ this.gatherViewsHere = gatherViewsHere;
}
/**
- * returns the visible column regions of the alignment
- *
- * @param selectedRegionOnly
- * true to just return the contigs intersecting with the selected
- * area
- * @return
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
*/
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+ public void scrollComplementaryAlignment()
{
- int[] viscontigs = null;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
+ /*
+ * Populate a SearchResults object with the mapped location to scroll to. If
+ * there is no complement, or it is not following highlights, or no mapping
+ * is found, the result will be empty.
+ */
+ SearchResultsI sr = new SearchResults();
+ int verticalOffset = findComplementScrollTarget(sr);
+ if (!sr.isEmpty())
{
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes() + 1;
+ // TODO would like next line without cast but needs more refactoring...
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+ .getAlignPanel();
+ complementPanel.setToScrollComplementPanel(false);
+ complementPanel.scrollToCentre(sr, verticalOffset);
+ complementPanel.setToScrollComplementPanel(true);
}
- else
- {
- end = alignment.getWidth();
- }
- viscontigs = colSel.getVisibleContigs(start, end);
- return viscontigs;
}
/**
- * get hash of undo and redo list for the alignment
+ * Answers true if no alignment holds a reference to the given mapping
*
- * @return long[] { historyList.hashCode, redoList.hashCode };
- */
- public long[] getUndoRedoHash()
- {
- // TODO: JAL-1126
- if (historyList == null || redoList == null)
- return new long[]
- { -1, -1 };
- return new long[]
- { historyList.hashCode(), this.redoList.hashCode() };
- }
-
- /**
- * test if a particular set of hashcodes are different to the hashcodes for
- * the undo and redo list.
- *
- * @param undoredo
- * the stored set of hashcodes as returned by getUndoRedoHash
- * @return true if the hashcodes differ (ie the alignment has been edited) or
- * the stored hashcode array differs in size
+ * @param acf
+ * @return
*/
- public boolean isUndoRedoHashModified(long[] undoredo)
+ protected boolean noReferencesTo(AlignedCodonFrame acf)
{
- if (undoredo == null)
- {
- return true;
- }
- long[] cstate = getUndoRedoHash();
- if (cstate.length != undoredo.length)
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames == null)
{
return true;
}
-
- for (int i = 0; i < cstate.length; i++)
+ for (AlignFrame af : frames)
{
- if (cstate[i] != undoredo[i])
+ if (!af.isClosed())
{
- return true;
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ AlignmentI al = ap.getAlignment();
+ if (al != null && al.getCodonFrames().contains(acf))
+ {
+ return false;
+ }
+ }
}
}
- return false;
- }
-
- public boolean getCentreColumnLabels()
- {
- return centreColumnLabels;
- }
-
- public void setCentreColumnLabels(boolean centrecolumnlabels)
- {
- centreColumnLabels = centrecolumnlabels;
- }
-
- /**
- * enable or disable the display of Database Cross References in the sequence
- * ID tooltip
- */
- public void setShowDbRefs(boolean show)
- {
- showdbrefs = show;
- }
-
- /**
- *
- * @return true if Database References are to be displayed on tooltips.
- */
- public boolean isShowDbRefs()
- {
- return showdbrefs;
- }
-
- /**
- *
- * @return true if Non-positional features are to be displayed on tooltips.
- */
- public boolean isShowNpFeats()
- {
- return shownpfeats;
+ return true;
}
/**
- * enable or disable the display of Non-Positional sequence features in the
- * sequence ID tooltip
+ * 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 show
+ * @param featureSettings
*/
- public void setShowNpFeats(boolean show)
+ @Override
+ public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
{
- shownpfeats = show;
+ 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.
*
- * @return true if view has hidden rows
+ * @param featureSettings
*/
- public boolean hasHiddenRows()
+ @Override
+ public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings)
{
- return hasHiddenRows;
+ 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.
*
- * @return true if view has hidden columns
- */
- public boolean hasHiddenColumns()
- {
- return hasHiddenColumns;
- }
-
- /**
- * when set, view will scroll to show the highlighted position
- */
- public boolean followHighlight = true;
-
- /**
- * @return true if view should scroll to show the highlighted region of a
- * sequence
- * @return
- */
- public boolean getFollowHighlight()
- {
- return followHighlight;
- }
-
- public boolean followSelection = true;
-
- /**
- * @return true if view selection should always follow the selections
- * broadcast by other selection sources
+ * @param featureSettings
+ * @param mergeOnly
*/
- public boolean getFollowSelection()
- {
- return followSelection;
- }
-
- boolean showSeqFeaturesHeight;
-
- public void sendSelection()
+ private void transferFeaturesStyles(FeatureSettingsModelI featureSettings,
+ boolean mergeOnly)
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance).sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
- }
-
- public void setShowSequenceFeaturesHeight(boolean selected)
- {
- showSeqFeaturesHeight = selected;
- }
-
- public boolean getShowSequenceFeaturesHeight()
- {
- return showSeqFeaturesHeight;
- }
-
- /**
- * return the alignPanel containing the given viewport. Use this to get the
- * components currently handling the given viewport.
- *
- * @param av
- * @return null or an alignPanel guaranteed to have non-null alignFrame
- * reference
- */
- public AlignmentPanel getAlignPanel()
- {
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
- .getSequenceSetId());
- AlignmentPanel ap = null;
- for (int p = 0; aps != null && p < aps.length; p++)
+ if (featureSettings == null)
{
- if (aps[p].av == this)
- {
- return aps[p];
- }
+ return;
}
- return null;
- }
-
- public boolean getSortByTree()
- {
- return sortByTree;
- }
- public void setSortByTree(boolean sort)
- {
- sortByTree = sort;
- }
-
- /**
- * 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))
+ FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+ List origRenderOrder = new ArrayList<>(),
+ 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();
+ if (!mergeOnly)
{
- if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+ // only clear displayed features if we are merging
+ 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
+ */
+ for (String type : renderOrder)
+ {
+ FeatureColourI preferredColour = featureSettings
+ .getFeatureColour(type);
+ FeatureColourI origColour = fr.getFeatureStyle(type);
+ if (!mergeOnly || (!origRenderOrder.contains(type)
+ || origColour == null
+ || (!origColour.isGraduatedColour()
+ && origColour.getColour() != null
+ && origColour.getColour().equals(
+ ColorUtils.createColourFromName(type)))))
{
- // do nothing
- return;
- }
- if (colSel == null)
+ // if we are merging, only update if there wasn't already a colour defined for
+ // this type
+ if (preferredColour != null)
{
- colSel = new ColumnSelection();
+ fr.setColour(type, preferredColour);
}
- for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ if (featureSettings.isFeatureDisplayed(type))
{
- colSel.addElement(cspos);
+ displayed.setVisible(type);
}
}
- }
-
- public StructureSelectionManager getStructureSelectionManager()
- {
- return StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- }
+ }
- /**
- *
- * @param pdbEntries
- * @return a series of SequenceI arrays, one for each PDBEntry, listing which
- * sequence in the alignment holds a reference to it
- */
- public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
- {
- ArrayList seqvectors = new ArrayList();
- for (PDBEntry pdb : pdbEntries)
+ /*
+ * set visibility of feature groups
+ */
+ for (String group : fr.getFeatureGroups())
{
- ArrayList seqs = new ArrayList();
- for (int i = 0; i < alignment.getHeight(); i++)
+ if (!mergeOnly || !origGroups.contains(group))
{
- Vector pdbs = alignment.getSequenceAt(i).getDatasetSequence()
- .getPDBId();
- if (pdbs == null)
- continue;
- SequenceI sq;
- for (int p = 0; p < pdbs.size(); p++)
- {
- PDBEntry p1 = (PDBEntry) pdbs.elementAt(p);
- if (p1.getId().equals(pdb.getId()))
- {
- if (!seqs.contains(sq = alignment.getSequenceAt(i)))
- seqs.add(sq);
-
- continue;
- }
- }
+ // when merging, display groups only if the aren't already marked as not visible
+ fr.setGroupVisibility(group,
+ featureSettings.isGroupDisplayed(group));
}
- seqvectors.add(seqs.toArray(new SequenceI[seqs.size()]));
}
- return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
- }
-
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
- }
-
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
- /**
- *
- * @return true if alignment characters should be displayed
- */
- public boolean isValidCharWidth()
- {
- return validCharWidth;
- }
-
- private Hashtable calcIdParams = new Hashtable();
-
- public AutoCalcSetting getCalcIdSettingsFor(String calcId)
- {
- return calcIdParams.get(calcId);
- }
- public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings,
- boolean needsUpdate)
- {
- calcIdParams.put(calcId, settings);
- // TODO: create a restart list to trigger any calculations that need to be
- // restarted after load
- // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
- if (needsUpdate)
+ /*
+ * order the features
+ */
+ if (featureSettings.optimiseOrder())
{
- Cache.log.debug("trigger update for " + calcId);
+ // TODO not supported (yet?)
+ }
+ else
+ {
+ fr.orderFeatures(featureSettings);
}
+ fr.setTransparency(featureSettings.getTransparency());
}
- public Hashtable getFeaturesDisplayed()
+ public String getViewName()
{
- return featuresDisplayed;
+ return viewName;
}
- public void setFeaturesDisplayed(Hashtable featuresDisplayed)
+ public void setViewName(String viewName)
{
- this.featuresDisplayed = featuresDisplayed;
+ this.viewName = viewName;
}
}