X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=b490a4b55d23f342f7c03af14f3962bcf3333517;hb=3ad26765f3e72cc506df226ac026034c9b20ce5d;hp=6397ba97bf2ecada2b2763fc8b4026fddb4225fd;hpb=e1e9f9f44944414e474ed500bc9e06f79dae76c7;p=jalview.git diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 6397ba9..b490a4b 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -22,7 +22,6 @@ package jalview.gui; import jalview.analysis.AlignmentUtils; import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; -import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureColourI; @@ -39,7 +38,6 @@ 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; @@ -72,13 +70,11 @@ import javax.swing.JInternalFrame; * @author $author$ * @version $Revision: 1.141 $ */ -public class AlignViewport extends AlignmentViewport implements - SelectionSource +public class AlignViewport extends AlignmentViewport + implements SelectionSource { Font font; - TreeModel currentTree = null; - boolean cursorMode = false; boolean antiAlias = false; @@ -130,8 +126,8 @@ public class AlignViewport extends AlignmentViewport implements // 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) { @@ -192,8 +188,8 @@ public class AlignViewport extends AlignmentViewport implements // 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) { @@ -226,17 +222,17 @@ 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() @@ -285,7 +281,11 @@ public class AlignViewport extends AlignmentViewport implements showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true); } initAutoAnnotation(); - String colourProperty = alignment.isNucleotide() ? Preferences.DEFAULT_COLOUR_NUC + initInformation(); + + + String colourProperty = alignment.isNucleotide() + ? Preferences.DEFAULT_COLOUR_NUC : Preferences.DEFAULT_COLOUR_PROT; String schemeName = Cache.getProperty(colourProperty); if (schemeName == null) @@ -294,8 +294,8 @@ 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 +311,6 @@ 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; /** @@ -486,27 +448,6 @@ public class AlignViewport extends AlignmentViewport implements } /** - * DOCUMENT ME! - * - * @param tree - * DOCUMENT ME! - */ - public void setCurrentTree(TreeModel tree) - { - currentTree = tree; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public TreeModel getCurrentTree() - { - return currentTree; - } - - /** * returns the visible column regions of the alignment * * @param selectedRegionOnly @@ -595,8 +536,8 @@ public class AlignViewport extends AlignmentViewport implements public void sendSelection() { jalview.structure.StructureSelectionManager - .getStructureSelectionManager(Desktop.instance).sendSelection( - new SequenceGroup(getSelectionGroup()), + .getStructureSelectionManager(Desktop.instance) + .sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), new HiddenColumns(getAlignment().getHiddenColumns()), this); @@ -612,8 +553,8 @@ 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) @@ -672,8 +613,7 @@ 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; @@ -754,7 +694,8 @@ public class AlignViewport extends AlignmentViewport implements * * * @param command @@ -875,8 +816,7 @@ 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, @@ -918,8 +858,9 @@ 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. @@ -936,8 +877,8 @@ 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) { } @@ -969,8 +910,8 @@ 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(); @@ -1161,6 +1102,4 @@ public class AlignViewport extends AlignmentViewport implements return normaliseHMMSequenceLogo; } - - }