X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=2005b91757de11968e32e4cff50d0280d8f63a5f;hb=refs%2Fheads%2Ffeatures%2Fhmmer_statistics;hp=3d0eb2128bbda96b59e7b585d0f8043029f7da63;hpb=46b2ffc28aeef5800f35ce31a742a65095e01621;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 3d0eb21..2005b91 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; @@ -35,6 +35,7 @@ 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; @@ -56,6 +57,7 @@ import jalview.ws.params.AutoCalcSetting; 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; @@ -75,7 +77,7 @@ public class AlignViewport extends AlignmentViewport implements { Font font; - NJTree currentTree = null; + TreeModel currentTree = null; boolean cursorMode = false; @@ -104,7 +106,7 @@ public class AlignViewport extends AlignmentViewport implements */ public AlignViewport(AlignmentI al) { - setAlignment(al); + super(al); init(); } @@ -122,6 +124,7 @@ 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 @@ -134,8 +137,8 @@ public class AlignViewport extends AlignmentViewport implements { Cache.log.debug("Setting viewport's view id : " + viewId); } - setAlignment(al); init(); + } /** @@ -146,12 +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(); } @@ -164,7 +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); @@ -180,9 +183,10 @@ 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 @@ -195,10 +199,10 @@ public class AlignViewport extends AlignmentViewport implements { Cache.log.debug("Setting viewport's view id : " + viewId); } - setAlignment(al); + if (hiddenColumns != null) { - colSel = hiddenColumns; + al.setHiddenColumns(hiddenColumns); } init(); } @@ -237,10 +241,6 @@ public class AlignViewport extends AlignmentViewport implements 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"); @@ -281,6 +281,8 @@ 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 @@ -350,23 +352,19 @@ public class AlignViewport extends AlignmentViewport implements boolean validCharWidth; /** - * update view settings with the given font. You may need to call - * alignPanel.fontChanged to update the layout geometry - * - * @param setGrid - * when true, charWidth/height is set according to font mentrics + * {@inheritDoc} */ + @Override public void setFont(Font f, boolean setGrid) { font = f; Container c = new Container(); - java.awt.FontMetrics fm = c.getFontMetrics(font); - int w = viewStyle.getCharWidth(), ww = fm.charWidth('M'), h = viewStyle - .getCharHeight(); if (setGrid) { + FontMetrics fm = c.getFontMetrics(font); + int ww = fm.charWidth('M'); setCharHeight(fm.getHeight()); setCharWidth(ww); } @@ -493,7 +491,7 @@ public class AlignViewport extends AlignmentViewport implements * @param tree * DOCUMENT ME! */ - public void setCurrentTree(NJTree tree) + public void setCurrentTree(TreeModel tree) { currentTree = tree; } @@ -503,7 +501,7 @@ public class AlignViewport extends AlignmentViewport implements * * @return DOCUMENT ME! */ - public NJTree getCurrentTree() + public TreeModel getCurrentTree() { return currentTree; } @@ -529,7 +527,7 @@ public class AlignViewport extends AlignmentViewport implements { end = alignment.getWidth(); } - viscontigs = colSel.getVisibleContigs(start, end); + viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end); return viscontigs; } @@ -599,7 +597,9 @@ public class AlignViewport extends AlignmentViewport implements jalview.structure.StructureSelectionManager .getStructureSelectionManager(Desktop.instance).sendSelection( new SequenceGroup(getSelectionGroup()), - new ColumnSelection(getColumnSelection()), this); + new ColumnSelection(getColumnSelection()), + new HiddenColumns(getAlignment().getHiddenColumns()), + this); } /** @@ -652,10 +652,10 @@ 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() @@ -708,6 +708,11 @@ public class AlignViewport extends AlignmentViewport implements normaliseSequenceLogo = state; } + public void setNormaliseHMMSequenceLogo(boolean state) + { + normaliseHMMSequenceLogo = state; + } + /** * * @return true if alignment characters should be displayed @@ -718,7 +723,7 @@ public class AlignViewport extends AlignmentViewport implements return validCharWidth; } - private Hashtable calcIdParams = new Hashtable(); + private Hashtable calcIdParams = new Hashtable<>(); public AutoCalcSetting getCalcIdSettingsFor(String calcId) { @@ -854,7 +859,7 @@ public class AlignViewport extends AlignmentViewport implements } } - setEndSeq(getAlignment().getHeight()); + ranges.setEndSeq(getAlignment().getHeight()); firePropertyChange("alignment", null, getAlignment().getSequences()); } @@ -1049,8 +1054,9 @@ 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); } } @@ -1148,4 +1154,11 @@ public class AlignViewport extends AlignmentViewport implements fr.setTransparency(featureSettings.getTransparency()); } + @Override + public boolean isNormaliseHMMSequenceLogo() + { + // TODO Auto-generated method stub + return normaliseHMMSequenceLogo; + } + }