X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=86dcbca4f955f6dff6a0c1750c5dc12077831224;hb=4c1ab51e2c08f85ba8c38486adf4a6ce0b0f25c3;hp=c1792c850faa937ba80e3b9a10a910287c721a65;hpb=4772c2b206c62f3e26e66cca8396ba031ff48b3e;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index c1792c8..86dcbca 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -22,7 +22,7 @@ package jalview.gui; import jalview.analysis.AlignmentUtils; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.analysis.NJTree; +import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureColourI; @@ -35,10 +35,10 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; -import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.renderer.ResidueShader; @@ -46,7 +46,6 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.ResidueColourScheme; import jalview.schemes.UserColourScheme; -import jalview.structure.CommandListener; import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; import jalview.structure.VamsasSource; @@ -61,6 +60,7 @@ import java.awt.FontMetrics; import java.awt.Rectangle; import java.util.ArrayList; import java.util.Hashtable; +import java.util.Iterator; import java.util.List; import java.util.Vector; @@ -72,12 +72,12 @@ import javax.swing.JInternalFrame; * @author $author$ * @version $Revision: 1.141 $ */ -public class AlignViewport extends AlignmentViewport implements - SelectionSource, CommandListener +public class AlignViewport extends AlignmentViewport + implements SelectionSource { Font font; - NJTree currentTree = null; + TreeModel currentTree = null; boolean cursorMode = false; @@ -106,7 +106,7 @@ public class AlignViewport extends AlignmentViewport implements */ public AlignViewport(AlignmentI al) { - setAlignment(al); + super(al); init(); } @@ -124,20 +124,21 @@ 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(); + } /** @@ -148,12 +149,12 @@ public class AlignViewport extends AlignmentViewport implements * @param hiddenColumns * ColumnSelection */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns) + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns) { - setAlignment(al); + super(al); if (hiddenColumns != null) { - colSel = hiddenColumns; + al.setHiddenColumns(hiddenColumns); } init(); } @@ -166,7 +167,7 @@ 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); @@ -182,25 +183,26 @@ public class AlignViewport extends AlignmentViewport implements * @param viewid * (may be null) */ - public AlignViewport(AlignmentI al, ColumnSelection hiddenColumns, + public AlignViewport(AlignmentI al, HiddenColumns hiddenColumns, String seqsetid, String viewid) { + super(al); sequenceSetID = seqsetid; viewId = viewid; // TODO remove these once 2.4.VAMSAS release finished if (Cache.log != null && Cache.log.isDebugEnabled() && seqsetid != null) { - 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) { - colSel = hiddenColumns; + al.setHiddenColumns(hiddenColumns); } init(); } @@ -224,25 +226,21 @@ public class AlignViewport extends AlignmentViewport implements setShowDBRefs(Cache.getDefault("SHOW_DBREFS_TOOLTIP", true)); viewStyle.setSeqNameItalics(Cache.getDefault("ID_ITALICS", true)); viewStyle.setWrapAlignment(Cache.getDefault("WRAP_ALIGNMENT", false)); - viewStyle.setShowUnconserved(Cache - .getDefault("SHOW_UNCONSERVED", false)); + viewStyle.setShowUnconserved( + Cache.getDefault("SHOW_UNCONSERVED", false)); sortByTree = Cache.getDefault("SORT_BY_TREE", false); followSelection = Cache.getDefault("FOLLOW_SELECTIONS", true); - sortAnnotationsBy = SequenceAnnotationOrder.valueOf(Cache.getDefault( - Preferences.SORT_ANNOTATIONS, - SequenceAnnotationOrder.NONE.name())); - showAutocalculatedAbove = Cache.getDefault( - Preferences.SHOW_AUTOCALC_ABOVE, false); - viewStyle.setScaleProteinAsCdna(Cache.getDefault( - Preferences.SCALE_PROTEIN_TO_CDNA, true)); + sortAnnotationsBy = SequenceAnnotationOrder + .valueOf(Cache.getDefault(Preferences.SORT_ANNOTATIONS, + SequenceAnnotationOrder.NONE.name())); + showAutocalculatedAbove = Cache + .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); + viewStyle.setScaleProteinAsCdna( + Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true)); } void init() { - this.startRes = 0; - this.endRes = alignment.getWidth() - 1; - this.startSeq = 0; - this.endSeq = alignment.getHeight() - 1; applyViewProperties(); String fontName = Cache.getDefault("FONT_NAME", "SansSerif"); @@ -283,9 +281,12 @@ public class AlignViewport extends AlignmentViewport implements false); showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); showConsensus = Cache.getDefault("SHOW_IDENTITY", true); + + showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true); } initAutoAnnotation(); - String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC + String colourProperty = alignment.isNucleotide() + ? Preferences.DEFAULT_COLOUR_NUC : Preferences.DEFAULT_COLOUR_PROT; String schemeName = Cache.getProperty(colourProperty); if (schemeName == null) @@ -294,8 +295,8 @@ public class AlignViewport extends AlignmentViewport implements schemeName = Cache.getDefault(Preferences.DEFAULT_COLOUR, ResidueColourScheme.NONE); } - ColourSchemeI colourScheme = ColourSchemeProperty.getColourScheme( - alignment, schemeName); + ColourSchemeI colourScheme = ColourSchemeProperty + .getColourScheme(alignment, schemeName); residueShading = new ResidueShader(colourScheme); if (colourScheme instanceof UserColourScheme) @@ -311,44 +312,6 @@ public class AlignViewport extends AlignmentViewport implements } } - /** - * 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 (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); - } - } - } - - SequenceI sq = new Sequence("Consensus", seqs.toString()); - sq.setDescription("Percentage Identity Consensus " - + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); - return sq; - } - boolean validCharWidth; /** @@ -491,7 +454,7 @@ public class AlignViewport extends AlignmentViewport implements * @param tree * DOCUMENT ME! */ - public void setCurrentTree(NJTree tree) + public void setCurrentTree(TreeModel tree) { currentTree = tree; } @@ -501,7 +464,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ - public NJTree getCurrentTree() + public TreeModel getCurrentTree() { return currentTree; } @@ -514,10 +477,10 @@ public class AlignViewport extends AlignmentViewport implements * area * @return */ - public int[] getViewAsVisibleContigs(boolean selectedRegionOnly) + public Iterator getViewAsVisibleContigs(boolean selectedRegionOnly) { - int[] viscontigs = null; - int start = 0, end = 0; + int start = 0; + int end = 0; if (selectedRegionOnly && selectionGroup != null) { start = selectionGroup.getStartRes(); @@ -527,8 +490,7 @@ public class AlignViewport extends AlignmentViewport implements { end = alignment.getWidth(); } - viscontigs = colSel.getVisibleContigs(start, end); - return viscontigs; + return (alignment.getHiddenColumns().getVisContigsIterator(start, end)); } /** @@ -595,9 +557,11 @@ public class AlignViewport extends AlignmentViewport implements public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance).sendSelection( - new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + .getStructureSelectionManager(Desktop.instance) + .sendSelection(new SequenceGroup(getSelectionGroup()), + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), + this); } /** @@ -610,8 +574,8 @@ public class AlignViewport extends AlignmentViewport implements */ public AlignmentPanel getAlignPanel() { - AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this - .getSequenceSetId()); + AlignmentPanel[] aps = PaintRefresher + .getAssociatedPanels(this.getSequenceSetId()); for (int p = 0; aps != null && p < aps.length; p++) { if (aps[p].av == this) @@ -650,10 +614,10 @@ public class AlignViewport extends AlignmentViewport implements */ public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries) { - List seqvectors = new ArrayList(); + List seqvectors = new ArrayList<>(); for (PDBEntry pdb : pdbEntries) { - List choosenSeqs = new ArrayList(); + List choosenSeqs = new ArrayList<>(); for (SequenceI sq : alignment.getSequences()) { Vector pdbRefEntries = sq.getDatasetSequence() @@ -670,8 +634,7 @@ public class AlignViewport extends AlignmentViewport implements && pdb.getChainCode() != null) { if (pdbRefEntry.getChainCode().equalsIgnoreCase( - pdb.getChainCode()) - && !choosenSeqs.contains(sq)) + pdb.getChainCode()) && !choosenSeqs.contains(sq)) { choosenSeqs.add(sq); continue; @@ -716,7 +679,7 @@ public class AlignViewport extends AlignmentViewport implements return validCharWidth; } - private Hashtable calcIdParams = new Hashtable(); + private Hashtable calcIdParams = new Hashtable<>(); public AutoCalcSetting getCalcIdSettingsFor(String calcId) { @@ -746,7 +709,8 @@ public class AlignViewport extends AlignmentViewport implements *
    *
  • compute the equivalent edit on the mapped sequences
    • *
  • apply the mapped edit
    • - *
  • 'apply' the source edit to the working copy of the source sequences
    • + *
  • 'apply' the source edit to the working copy of the source + * sequences
    • *
* * @param command @@ -852,7 +816,7 @@ public class AlignViewport extends AlignmentViewport implements } } - setEndSeq(getAlignment().getHeight()); + ranges.setEndSeq(getAlignment().getHeight()); firePropertyChange("alignment", null, getAlignment().getSequences()); } @@ -867,8 +831,7 @@ public class AlignViewport extends AlignmentViewport implements */ protected boolean openLinkedAlignment(AlignmentI al, String title) { - String[] options = new String[] { - MessageManager.getString("action.no"), + String[] options = new String[] { MessageManager.getString("action.no"), MessageManager.getString("label.split_window"), MessageManager.getString("label.new_window"), }; final String question = JvSwingUtils.wrapTooltip(true, @@ -910,8 +873,9 @@ public class AlignViewport extends AlignmentViewport implements AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); newAlignFrame.setTitle(title); - newAlignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", new Object[] { title })); + newAlignFrame.statusBar.setText(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. @@ -928,8 +892,8 @@ public class AlignViewport extends AlignmentViewport implements try { - newAlignFrame.setMaximum(jalview.bin.Cache.getDefault( - "SHOW_FULLSCREEN", false)); + newAlignFrame.setMaximum( + jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -961,8 +925,8 @@ public class AlignViewport extends AlignmentViewport implements * is protein, the mappings to cDNA will be registered with * StructureSelectionManager as a side-effect. */ - AlignFrame copyMe = new AlignFrame(complement, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); copyMe.setTitle(getAlignPanel().alignFrame.getTitle()); AlignmentI al = newAlignFrame.viewport.getAlignment(); @@ -1047,8 +1011,9 @@ public class AlignViewport extends AlignmentViewport implements // TODO would like next line without cast but needs more refactoring... final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement()) .getAlignPanel(); - complementPanel.setDontScrollComplement(true); + complementPanel.setToScrollComplementPanel(false); complementPanel.scrollToCentre(sr, verticalOffset); + complementPanel.setToScrollComplementPanel(true); } }