/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
*
- * 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.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
/*
* Jalview - A Sequence Alignment Editor and Viewer
import jalview.schemes.*;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision$
*/
-public class AlignViewport implements SelectionSource
+public class AlignViewport implements SelectionSource, VamsasSource
{
private static final int RIGHT_JUSTIFY = 1;
boolean cursorMode = false;
/**
- * Keys are the feature types which are
- * currently visible. Note: Values are not used!
+ * Keys are the feature types which are currently visible. Note: Values are
+ * not used!
*/
Hashtable featuresDisplayed = null;
AlignmentAnnotation conservation;
AlignmentAnnotation quality;
+
AlignmentAnnotation[] groupConsensus;
+
AlignmentAnnotation[] groupConservation;
-
+
boolean autoCalculateConsensus = true;
/** DOCUMENT ME!! */
/**
* Creates a new AlignViewport object.
*
- * @param al alignment to view
+ * @param al
+ * alignment to view
*/
public AlignViewport(AlignmentI al)
{
setAlignment(al);
init();
}
+
/**
* Create a new AlignViewport object with a specific sequence set ID
+ *
* @param al
- * @param seqsetid (may be null - but potential for ambiguous constructor exception)
+ * @param seqsetid
+ * (may be null - but potential for ambiguous constructor exception)
*/
public AlignViewport(AlignmentI al, String seqsetid)
{
- this(al,seqsetid,null);
+ this(al, seqsetid, null);
}
+
public AlignViewport(AlignmentI al, String seqsetid, String viewid)
{
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); }
- if (Cache.log!=null && Cache.log.isDebugEnabled() && viewId!=null) { Cache.log.debug("Setting viewport's view id : "+viewId); }
+ if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ {
+ 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();
}
* Create a new AlignViewport with hidden regions
*
* @param al
- * AlignmentI
+ * AlignmentI
* @param hiddenColumns
- * ColumnSelection
+ * ColumnSelection
*/
public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns)
{
if (hiddenColumns != null)
{
this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null && hiddenColumns.getHiddenColumns().size()>0)
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
{
hasHiddenColumns = true;
- } else {
+ }
+ else
+ {
hasHiddenColumns = false;
}
}
init();
}
+
/**
* New viewport with hidden columns and an existing sequence set id
+ *
* @param al
* @param hiddenColumns
- * @param seqsetid (may be null)
+ * @param seqsetid
+ * (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid)
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ String seqsetid)
{
- this(al,hiddenColumns,seqsetid,null);
+ this(al, hiddenColumns, seqsetid, null);
}
+
/**
* New viewport with hidden columns and an existing sequence set id and viewid
+ *
* @param al
* @param hiddenColumns
- * @param seqsetid (may be null)
- * @param viewid (may be null)
+ * @param seqsetid
+ * (may be null)
+ * @param viewid
+ * (may be null)
*/
- public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, String seqsetid, String viewid)
+ public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns,
+ String seqsetid, String viewid)
{
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); }
- if (Cache.log!=null && Cache.log.isDebugEnabled() && viewId!=null) { Cache.log.debug("Setting viewport's view id : "+viewId); }
+ if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null)
+ {
+ 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)
+ if (hiddenColumns.getHiddenColumns() != null
+ && hiddenColumns.getHiddenColumns().size() > 0)
{
hasHiddenColumns = true;
- } else {
+ }
+ else
+ {
hasHiddenColumns = false;
}
}
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
padGaps = Cache.getDefault("PAD_GAPS", true);
- shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP",true);
- showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP",true);
-
+ shownpfeats = Cache.getDefault("SHOW_NPFEATS_TOOLTIP", true);
+ showdbrefs = Cache.getDefault("SHOW_DBREFS_TOOLTIP", true);
+
String fontName = Cache.getDefault("FONT_NAME", "SansSerif");
String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "");
String fontSize = Cache.getDefault("FONT_SIZE", "10");
alignment.addAnnotation(quality);
}
- showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION", false);
-
+ showGroupConservation = Cache.getDefault("SHOW_GROUP_CONSERVATION",
+ false);
+
{
-
+
}
}
- showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM", true);
+ showConsensusHistogram = Cache.getDefault("SHOW_CONSENSUS_HISTOGRAM",
+ true);
showSequenceLogo = Cache.getDefault("SHOW_CONSENSUS_LOGO", false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
- // TODO: add menu option action that nulls or creates consensus object depending on if the user wants to see the annotation or not in a specific alignment
+ // TODO: add menu option action that nulls or creates consensus object
+ // depending on if the user wants to see the annotation or not in a
+ // specific alignment
consensus = new AlignmentAnnotation("Consensus", "PID",
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
consensus.hasText = true;
}
wrapAlignment = jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false);
- showUnconserved = jalview.bin.Cache.getDefault("SHOW_UNCONSERVED", 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);
}
/**
* set the flag
*
* @param b
- * features are displayed if true
+ * features are displayed if true
*/
public void setShowSequenceFeatures(boolean b)
{
private boolean shownpfeats;
/**
- * consensus annotation includes all percentage for all symbols in column
- */
- private boolean includeAllConsensusSymbols=true;
-
- /**
* trigger update of conservation annotation
*/
public void updateConservation(final AlignmentPanel ap)
{
// see note in mantis : issue number 8585
- if (alignment.isNucleotide() || conservation == null || !autoCalculateConsensus)
+ if (alignment.isNucleotide() || conservation == null
+ || !autoCalculateConsensus)
{
return;
}
try
{
- int aWidth = (alignment != null) ? alignment.getWidth() : 0; // null
- // pointer
- // possibility
- // here.
- if (aWidth < 0)
+ int aWidth = (alignment != null) ? alignment.getWidth() : -1; // null
+ // pointer
+ // possibility
+ // here.
+ if (aWidth <= 0)
{
+ updatingConsensus = false;
+ UPDATING_CONSENSUS = false;
return;
}
consensus.annotations = new Annotation[aWidth];
hconsensus = new Hashtable[aWidth];
- AAFrequency.calculate(alignment.getSequencesArray(), 0, alignment
- .getWidth(), hconsensus, includeAllConsensusSymbols);
- AAFrequency.completeConsensus(consensus,hconsensus,0,aWidth,ignoreGapsInConsensusCalculation, includeAllConsensusSymbols);
-
+ AAFrequency.calculate(alignment.getSequencesArray(), 0,
+ alignment.getWidth(), hconsensus, true);
+ updateAnnotation(true);
+
if (globalColourScheme != null)
{
globalColourScheme.setConsensus(hconsensus);
ap.paintAlignment(true);
}
}
+
+ /**
+ * update the consensus annotation from the sequence profile data using
+ * current visualization settings.
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(false);
+ }
+
+ protected void updateAnnotation(boolean immediate)
+ {
+ // TODO: make calls thread-safe, so if another thread calls this method,
+ // it will either return or wait until one calculation is finished.
+ if (immediate
+ || (!updatingConsensus && consensus != null && hconsensus != null))
+ {
+ AAFrequency.completeConsensus(consensus, hconsensus, 0,
+ hconsensus.length, ignoreGapsInConsensusCalculation,
+ showSequenceLogo);
+ }
+ }
}
/**
* DOCUMENT ME!
*
* @param sg
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setSelectionGroup(SequenceGroup sg)
{
- selectionGroup = sg;
+ selectionGroup = sg;
}
/**
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setConservationSelected(boolean b)
{
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setAbovePIDThreshold(boolean b)
{
* DOCUMENT ME!
*
* @param cs
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setGlobalColourScheme(ColourSchemeI cs)
{
* DOCUMENT ME!
*
* @param res
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setStartRes(int res)
{
* DOCUMENT ME!
*
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setStartSeq(int seq)
{
* DOCUMENT ME!
*
* @param res
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setEndRes(int res)
{
* DOCUMENT ME!
*
* @param seq
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setEndSeq(int seq)
{
* DOCUMENT ME!
*
* @param f
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setFont(Font f)
{
* DOCUMENT ME!
*
* @param w
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setCharWidth(int w)
{
* DOCUMENT ME!
*
* @param h
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setCharHeight(int h)
{
* DOCUMENT ME!
*
* @param w
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setWrappedWidth(int w)
{
* DOCUMENT ME!
*
* @param align
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setAlignment(AlignmentI align)
{
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setWrapAlignment(boolean state)
{
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setShowText(boolean state)
{
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setRenderGaps(boolean state)
{
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setColourText(boolean state)
{
* DOCUMENT ME!
*
* @param state
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setShowBoxes(boolean state)
{
* DOCUMENT ME!
*
* @param gap
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setGapCharacter(char gap)
{
* DOCUMENT ME!
*
* @param thresh
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setThreshold(int thresh)
{
* DOCUMENT ME!
*
* @param inc
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setIncrement(int inc)
{
* DOCUMENT ME!
*
* @param tree
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setCurrentTree(NJTree tree)
{
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setColourAppliesToAllGroups(boolean b)
{
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setShowJVSuffix(boolean b)
{
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setShowAnnotation(boolean b)
{
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setScaleAboveWrapped(boolean b)
{
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setScaleLeftWrapped(boolean b)
{
* DOCUMENT ME!
*
* @param b
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void setScaleRightWrapped(boolean b)
{
* Property change listener for changes in alignment
*
* @param listener
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void addPropertyChangeListener(
java.beans.PropertyChangeListener listener)
* DOCUMENT ME!
*
* @param listener
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void removePropertyChangeListener(
java.beans.PropertyChangeListener listener)
* Property change listener for changes in alignment
*
* @param prop
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param oldvalue
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param newvalue
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void firePropertyChange(String prop, Object oldvalue,
Object newvalue)
for (int i = 0; i < sequences.length; i++)
{
sequences[i] = new Sequence(sequences[i], annots); // construct new
- // sequence with
- // subset of visible
- // annotation
+ // sequence with
+ // subset of visible
+ // annotation
}
}
else
*/
public SequenceI[] getSequenceSelection()
{
- SequenceI[] sequences=null;
- if (selectionGroup!=null)
+ SequenceI[] sequences = null;
+ if (selectionGroup != null)
{
sequences = selectionGroup.getSequencesInOrder(alignment);
}
public jalview.datamodel.CigarArray getViewAsCigars(
boolean selectedRegionOnly)
{
- CigarArray selection = null;
- SequenceI[] seqs = null;
- int i, iSize;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- iSize = selectionGroup.getSize();
- seqs = selectionGroup.getSequencesInOrder(alignment);
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes(); // inclusive for start and end in
- // SeqCigar constructor
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth() - 1;
- }
- SeqCigar[] selseqs = new SeqCigar[iSize];
- for (i = 0; i < iSize; i++)
- {
- selseqs[i] = new SeqCigar(seqs[i], start, end);
- }
- selection = new CigarArray(selseqs);
- // now construct the CigarArray operations
- if (hasHiddenColumns)
- {
- Vector regions = colSel.getHiddenColumns();
- int[] region;
- int hideStart, hideEnd;
- int last = start;
- for (int j = 0; last < end & j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
- // edit hidden regions to selection range
- if (hideStart < last)
- {
- if (hideEnd > last)
- {
- hideStart = last;
- }
- else
- {
- continue;
- }
- }
-
- if (hideStart > end)
- {
- break;
- }
-
- if (hideEnd > end)
- {
- hideEnd = end;
- }
-
- if (hideStart > hideEnd)
- {
- break;
- }
- /**
- * form operations...
- */
- if (last < hideStart)
- {
- selection.addOperation(CigarArray.M, hideStart - last);
- }
- selection.addOperation(CigarArray.D, 1 + hideEnd - hideStart);
- last = hideEnd + 1;
- }
- // Final match if necessary.
- if (last < end)
- {
- selection.addOperation(CigarArray.M, end - last + 1);
- }
- }
- else
- {
- selection.addOperation(CigarArray.M, end - start + 1);
- }
- return selection;
+ return new jalview.datamodel.CigarArray(alignment, (hasHiddenColumns ? colSel : null), (selectedRegionOnly ? selectionGroup : null));
}
/**
* to an analysis function
*
* @param selectedOnly
- * boolean true to just return the selected view
+ * boolean true to just return the selected view
* @return AlignmentView
*/
- jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
+ public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
{
- // JBPNote:
- // this is here because the AlignmentView constructor modifies the
- // CigarArray
- // object. Refactoring of Cigar and alignment view representation should
- // be done to remove redundancy.
- CigarArray aligview = getViewAsCigars(selectedOnly);
- if (aligview != null)
- {
- return new AlignmentView(aligview,
- (selectedOnly && selectionGroup != null) ? selectionGroup
- .getStartRes() : 0);
- }
- return null;
+ return getAlignmentView(selectedOnly, false);
+ }
+
+ /**
+ * return a compact representation of the current alignment selection to pass
+ * to an analysis function
+ *
+ * @param selectedOnly
+ * boolean true to just return the selected view
+ * @param markGroups
+ * boolean true to annotate the alignment view with groups on the alignment (and intersecting with selected region if selectedOnly is true)
+ * @return AlignmentView
+ */
+ public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups)
+ {
+ return new AlignmentView(alignment, colSel, selectionGroup, hasHiddenColumns, selectedOnly, markGroups);
}
/**
return sequenceSetID;
}
+
/**
- * unique viewId for synchronizing state with stored Jalview Project
+ * unique viewId for synchronizing state with stored Jalview Project
*
*/
- private String viewId=null;
+ private String viewId = null;
-
public String getViewId()
{
- if (viewId==null)
+ if (viewId == null)
{
- viewId = this.getSequenceSetId()+"."+this.hashCode()+"";
+ viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
}
return viewId;
}
-
+
public void alignmentChanged(AlignmentPanel ap)
{
if (padGaps)
{
Alignment al = (Alignment) alignment;
Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0, al
- .getWidth() - 1);
+ ResidueProperties.propHash, 3, al.getSequences(), 0,
+ al.getWidth() - 1);
c.calculate();
c.verdict(false, ConsPercGaps);
SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
{
- ((ClustalxColourScheme) sg.cs).resetClustalX(sg
- .getSequences(hiddenRepSequences), sg.getWidth());
+ ((ClustalxColourScheme) sg.cs).resetClustalX(
+ sg.getSequences(hiddenRepSequences), sg.getWidth());
}
sg.recalcConservation();
}
* returns the visible column regions of the alignment
*
* @param selectedRegionOnly
- * true to just return the contigs intersecting with the
- * selected area
+ * true to just return the contigs intersecting with the selected
+ * area
* @return
*/
public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
* the undo and redo list.
*
* @param undoredo
- * the stored set of hashcodes as returned by getUndoRedoHash
+ * 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
*/
}
/**
- * enable or disable the display of Database Cross References in the sequence ID tooltip
- */
+ * enable or disable the display of Database Cross References in the sequence
+ * ID tooltip
+ */
public void setShowDbRefs(boolean show)
{
- showdbrefs=show;
+ showdbrefs = show;
}
/**
{
return shownpfeats;
}
+
/**
- * enable or disable the display of Non-Positional sequence features in the sequence ID tooltip
- * @param show
+ * enable or disable the display of Non-Positional sequence features in the
+ * sequence ID tooltip
+ *
+ * @param show
*/
public void setShowNpFeats(boolean show)
{
- shownpfeats=show;
+ shownpfeats = show;
}
+
/**
*
* @return true if view has hidden rows
{
return hasHiddenRows;
}
+
/**
*
* @return true if view has hidden columns
{
return hasHiddenColumns;
}
+
/**
* when set, view will scroll to show the highlighted position
*/
- public boolean followHighlight=true;
+ public boolean followHighlight = true;
+
/**
- * @return true if view should scroll to show the highlighted region of a sequence
+ * @return true if view should scroll to show the highlighted region of a
+ * sequence
* @return
*/
- public boolean getFollowHighlight() {
+ public boolean getFollowHighlight()
+ {
return followHighlight;
}
- public boolean followSelection=true;
+
+ public boolean followSelection = true;
+
/**
- * @return true if view selection should always follow the selections broadcast by other selection sources
+ * @return true if view selection should always follow the selections
+ * broadcast by other selection sources
*/
- public boolean getFollowSelection() {
+ public boolean getFollowSelection()
+ {
return followSelection;
}
- private long sgrouphash=-1,colselhash=-1;
+
+ private long sgrouphash = -1, colselhash = -1;
boolean showSeqFeaturesHeight;
+
/**
- * checks current SelectionGroup against record of last hash value, and updates record.
+ * checks current SelectionGroup against record of last hash value, and
+ * updates record.
+ *
* @return true if SelectionGroup changed since last call
*/
- boolean isSelectionGroupChanged() {
- int hc=(selectionGroup==null) ? -1 : selectionGroup.hashCode();
- if (hc!=sgrouphash)
+ boolean isSelectionGroupChanged()
+ {
+ int hc = (selectionGroup == null) ? -1 : selectionGroup.hashCode();
+ if (hc != sgrouphash)
{
sgrouphash = hc;
return true;
}
return false;
}
+
/**
- * checks current colsel against record of last hash value, and updates record.
+ * checks current colsel against record of last hash value, and updates
+ * record.
+ *
* @return true if colsel changed since last call
*/
- boolean isColSelChanged() {
- int hc=(colSel==null) ? -1 : colSel.hashCode();
- if (hc!=colselhash)
+ boolean isColSelChanged()
+ {
+ int hc = (colSel == null) ? -1 : colSel.hashCode();
+ if (hc != colselhash)
{
colselhash = hc;
return true;
}
return false;
}
+
public void sendSelection()
{
- jalview.structure.StructureSelectionManager.getStructureSelectionManager().sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this);
+ jalview.structure.StructureSelectionManager
+ .getStructureSelectionManager().sendSelection(
+ new SequenceGroup(getSelectionGroup()),
+ new ColumnSelection(getColumnSelection()), this);
}
+
public void setShowSequenceFeaturesHeight(boolean selected)
{
- showSeqFeaturesHeight = selected;
+ showSeqFeaturesHeight = selected;
}
+
public boolean getShowSequenceFeaturesHeight()
{
- return showSeqFeaturesHeight;
+ return showSeqFeaturesHeight;
}
- boolean showUnconserved=false;
+
+ boolean showUnconserved = false;
+
public boolean getShowUnconserved()
{
return showUnconserved;
}
+
public void setShowUnconserved(boolean showunconserved)
{
- showUnconserved=showunconserved;
+ showUnconserved = showunconserved;
}
+
/**
* 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
+ * @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++)
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this
+ .getSequenceSetId());
+ AlignmentPanel ap = null;
+ for (int p = 0; aps != null && p < aps.length; p++)
{
if (aps[p].av == this)
{
}
return null;
}
+
public boolean getSortByTree()
{
return sortByTree;
}
- public void setSortByTree(boolean sort) {
+
+ public void setSortByTree(boolean sort)
+ {
sortByTree = sort;
}
+
/**
* should conservation rows be shown for groups
*/
boolean showGroupConservation = false;
+
/**
* should consensus rows be shown for groups
*/
boolean showGroupConsensus = false;
+
/**
* should consensus profile be rendered by default
*/
public boolean showSequenceLogo = false;
+
/**
* should consensus histograms be rendered by default
*/
public boolean showConsensusHistogram = true;
+
/**
* @return the showConsensusProfile
*/
{
return showSequenceLogo;
}
+
/**
- * @param showSequenceLogo the new value
+ * @param showSequenceLogo
+ * the new value
*/
public void setShowSequenceLogo(boolean showSequenceLogo)
{
+ if (showSequenceLogo != this.showSequenceLogo)
+ {
+ // TODO: decouple settings setting from calculation when refactoring
+ // annotation update method from alignframe to viewport
+ this.showSequenceLogo = showSequenceLogo;
+ if (consensusThread != null)
+ {
+ consensusThread.updateAnnotation();
+ }
+ }
this.showSequenceLogo = showSequenceLogo;
}
+
/**
- * @param showConsensusHistogram the showConsensusHistogram to set
+ * @param showConsensusHistogram
+ * the showConsensusHistogram to set
*/
public void setShowConsensusHistogram(boolean showConsensusHistogram)
{
this.showConsensusHistogram = showConsensusHistogram;
}
-
+
/**
* @return the showGroupConservation
*/
{
return showGroupConservation;
}
+
/**
- * @param showGroupConservation the showGroupConservation to set
+ * @param showGroupConservation
+ * the showGroupConservation to set
*/
public void setShowGroupConservation(boolean showGroupConservation)
{
this.showGroupConservation = showGroupConservation;
}
+
/**
* @return the showGroupConsensus
*/
{
return showGroupConsensus;
}
+
/**
- * @param showGroupConsensus the showGroupConsensus to set
+ * @param showGroupConsensus
+ * the showGroupConsensus to set
*/
public void setShowGroupConsensus(boolean showGroupConsensus)
{
this.showGroupConsensus = showGroupConsensus;
}
+
/**
- * @return the includeAllConsensusSymbols
- */
- public boolean isIncludeAllConsensusSymbols()
- {
- return includeAllConsensusSymbols;
- }
- /**
- * @param includeAllConsensusSymbols the includeAllConsensusSymbols to set
+ *
+ * @return flag to indicate if the consensus histogram should be rendered by
+ * default
*/
- public void setIncludeAllConsensusSymbols(boolean includeAllConsensusSymbols)
+ public boolean isShowConsensusHistogram()
{
- this.includeAllConsensusSymbols = includeAllConsensusSymbols;
+ return this.showConsensusHistogram;
}
-
+
/**
+ * 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.
*
- * @return flag to indicate if the consensus histogram should be rendered by default
+ * @param sg
+ * @param wholewidth
*/
- public boolean isShowConsensusHistogram()
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
{
- return this.showConsensusHistogram;
+ 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);
+ }
+ }
}
-
}
git://source.jalview.org / jalview.git / blobdiff