- /**
- * 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
- * @return AlignmentView
- */
- public jalview.datamodel.AlignmentView getAlignmentView(boolean selectedOnly)
- {
- 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);
- }
-
- /**
- * This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. Use this for
- * calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
- *
- * @return String[]
- */
- public String[] getViewAsString(boolean selectedRegionOnly)
- {
- String[] 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() + 1;
- }
- else
- {
- iSize = alignment.getHeight();
- seqs = alignment.getSequencesArray();
- end = alignment.getWidth();
- }
-
- selection = new String[iSize];
- if (hasHiddenColumns)
- {
- selection = colSel.getVisibleSequenceStrings(start, end, seqs);
- }
- else
- {
- for (i = 0; i < iSize; i++)
- {
- selection[i] = seqs[i].getSequenceAsString(start, end);
- }
-
- }
- return selection;
- }
-
- public int[][] getVisibleRegionBoundaries(int min, int max)
- {
- Vector regions = new Vector();
- int start = min;
- int end = max;
-
- do
- {
- if (hasHiddenColumns)
- {
- if (start == 0)
- {
- start = colSel.adjustForHiddenColumns(start);
- }
-
- end = colSel.getHiddenBoundaryRight(start);
- if (start == end)
- {
- end = max;
- }
- if (end > max)
- {
- end = max;
- }
- }
-
- regions.addElement(new int[]
- { start, end });
-
- if (hasHiddenColumns)
- {
- start = colSel.adjustForHiddenColumns(end);
- start = colSel.getHiddenBoundaryLeft(start) + 1;
- }
- } while (end < max);
-
- int[][] startEnd = new int[regions.size()][2];
-
- regions.copyInto(startEnd);
-
- return startEnd;
-
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
-
- public String getSequenceSetId()
- {
- if (sequenceSetID == null)
- {
- sequenceSetID = alignment.hashCode() + "";
- }
-
- return sequenceSetID;
- }
-
- /**
- * unique viewId for synchronizing state with stored Jalview Project
- *
- */
- private String viewId = null;
-
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
- }
- return viewId;
- }
-
- public void alignmentChanged(AlignmentPanel ap)
- {
- if (padGaps)
- {
- alignment.padGaps();
- }
- if (hconsensus != null && autoCalculateConsensus)
- {
- updateConservation(ap);
- }
- if (autoCalculateConsensus)
- {
- updateConsensus(ap);
- }
-
- // Reset endRes of groups if beyond alignment width
- int alWidth = alignment.getWidth();
- Vector groups = alignment.getGroups();
- if (groups != null)
- {
- for (int i = 0; i < groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if (sg.getEndRes() > alWidth)
- {
- sg.setEndRes(alWidth - 1);
- }
- }
- }
-
- if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
- {
- selectionGroup.setEndRes(alWidth - 1);
- }
-
- resetAllColourSchemes();
-
- // alignment.adjustSequenceAnnotations();
- }
-
- void resetAllColourSchemes()
- {
- ColourSchemeI cs = globalColourScheme;
- if (cs != null)
- {
- if (cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
- alignment.getWidth());
- }
-
- cs.setConsensus(hconsensus);
- if (cs.conservationApplied())
- {
- Alignment al = (Alignment) alignment;
- Conservation c = new Conservation("All",
- ResidueProperties.propHash, 3, al.getSequences(), 0,
- al.getWidth() - 1);
- c.calculate();
- c.verdict(false, ConsPercGaps);
-
- cs.setConservation(c);
- }
- }
-
- int s, sSize = alignment.getGroups().size();
- for (s = 0; s < sSize; s++)
- {
- SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
- if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) sg.cs).resetClustalX(
- sg.getSequences(hiddenRepSequences), sg.getWidth());
- }
- sg.recalcConservation();
- }
- }
-
- public Color getSequenceColour(SequenceI seq)
- {
- if (sequenceColours == null || !sequenceColours.containsKey(seq))
- {
- return Color.white;
- }
- else
- {
- return (Color) sequenceColours.get(seq);
- }
- }
-
- public void setSequenceColour(SequenceI seq, Color col)
- {
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
- if (col == null)
- {
- sequenceColours.remove(seq);
- }
- else
- {
- sequenceColours.put(seq, col);
- }
- }
-
- /**
- * 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 };
- */
- public long[] getUndoRedoHash()
- {
- 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
- */
- public boolean isUndoRedoHashModified(long[] undoredo)
- {
- if (undoredo == null)
- {
- return true;
- }
- long[] cstate = getUndoRedoHash();
- if (cstate.length != undoredo.length)
- {
- return true;
- }
-
- for (int i = 0; i < cstate.length; i++)
- {
- if (cstate[i] != undoredo[i])
- {
- return true;
- }
- }
- return false;
- }
-
- public boolean getCentreColumnLabels()
- {
- return centreColumnLabels;
- }
-
- public void setCentreColumnLabels(boolean centrecolumnlabels)
- {
- centreColumnLabels = centrecolumnlabels;
- }
-
- public void updateSequenceIdColours()
- {
- Vector groups = alignment.getGroups();
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
- for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
- if (sg.idColour != null)
- {
- Vector sqs = sg.getSequences(hiddenRepSequences);
- for (int s = 0, sSize = sqs.size(); s < sSize; s++)
- {
- sequenceColours.put(sqs.elementAt(s), sg.idColour);
- }
- }
- }
- }
-
- /**
- * 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;
- }
-
- /**
- * enable or disable the display of Non-Positional sequence features in the
- * sequence ID tooltip
- *
- * @param show
- */
- public void setShowNpFeats(boolean show)
- {
- shownpfeats = show;
- }
-
- /**
- *
- * @return true if view has hidden rows
- */
- public boolean hasHiddenRows()
- {
- return hasHiddenRows;
- }
-
- /**
- *
- * @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
- */
- public boolean getFollowSelection()
- {
- return followSelection;
- }
-
- private long sgrouphash = -1, colselhash = -1;
-
- boolean showSeqFeaturesHeight;
-
- /**
- * checks current SelectionGroup against record of last hash value, and
- * updates record.
- * @param b update the record of last hash value
- *
- * @return true if SelectionGroup changed since last call (when b is true)
- */
- boolean isSelectionGroupChanged(boolean b)
- {
- int hc = (selectionGroup == null || selectionGroup.getSize()==0) ? -1 : selectionGroup.hashCode();
- if (hc!=-1 && hc != sgrouphash)
- {
- if (b) {sgrouphash = hc;}
- return true;
- }
- return false;
- }
-
- /**
- * checks current colsel against record of last hash value, and optionally updates
- * record.
-
- * @param b update the record of last hash value
- * @return true if colsel changed since last call (when b is true)
- */
- boolean isColSelChanged(boolean b)
- {
- int hc = (colSel == null || colSel.size()==0) ? -1 : colSel.hashCode();
- if (hc!=-1 && hc != colselhash)
- {
- if (b) {colselhash = hc;}
- return true;
- }
- return false;
- }
-
- public void sendSelection()
- {
- 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;
- }
-
- boolean showUnconserved = false;
-
- public boolean getShowUnconserved()
- {
- return showUnconserved;
- }
-
- public void setShowUnconserved(boolean 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
- */
- public AlignmentPanel getAlignPanel()
- {
- 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 aps[p];
- }
- }
- return null;
- }
-
- public boolean getSortByTree()
- {
- return sortByTree;
- }
-
- 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
- */
- public boolean isShowSequenceLogo()
- {
- return showSequenceLogo;
- }
-
- /**
- * @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
- */
- public void setShowConsensusHistogram(boolean showConsensusHistogram)
- {
- this.showConsensusHistogram = showConsensusHistogram;
- }
-
- /**
- * @return the showGroupConservation
- */
- public boolean isShowGroupConservation()
- {
- return showGroupConservation;
- }
-
- /**
- * @param showGroupConservation
- * the showGroupConservation to set
- */
- public void setShowGroupConservation(boolean showGroupConservation)
- {
- this.showGroupConservation = showGroupConservation;
- }
-
- /**
- * @return the showGroupConsensus
- */
- public boolean isShowGroupConsensus()
- {
- return showGroupConsensus;
- }
-
- /**
- * @param showGroupConsensus
- * the showGroupConsensus to set
- */
- public void setShowGroupConsensus(boolean showGroupConsensus)
- {
- this.showGroupConsensus = showGroupConsensus;
- }
-
- /**
- *
- * @return flag to indicate if the consensus histogram should be rendered by
- * default
- */
- public boolean isShowConsensusHistogram()
- {
- 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.
- *
- * @param sg
- * @param wholewidth
- */
- public void expandColSelection(SequenceGroup sg, boolean wholewidth)
- {
- int sgs, sge;
- if (sg != null
- && (sgs = sg.getStartRes()) >= 0
- && sg.getStartRes() <= (sge = sg.getEndRes())
- && (colSel == null || colSel.getSelected() == null || colSel
- .getSelected().size() == 0))
- {
- if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
- {
- // do nothing
- return;
- }
- if (colSel == null)
- {
- colSel = new ColumnSelection();
- }
- for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
- {
- colSel.addElement(cspos);
- }
- }
- }
-
- public StructureSelectionManager getStructureSelectionManager()
- {
- return StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
- }