From f12e846651e7564aa39b35ce7d6a18a929baeb4c Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 20 Feb 2015 11:53:18 +0000 Subject: [PATCH] JAL-1665 create dataset sequences in applet --- src/jalview/appletgui/CutAndPasteTransfer.java | 254 ++++++++++++-------- src/jalview/datamodel/Sequence.java | 19 +- .../renderer/seqfeatures/FeatureRenderer.java | 19 +- .../seqfeatures/FeatureRendererModel.java | 4 +- 4 files changed, 175 insertions(+), 121 deletions(-) diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java index 0a9ca56..0c717b2 100644 --- a/src/jalview/appletgui/CutAndPasteTransfer.java +++ b/src/jalview/appletgui/CutAndPasteTransfer.java @@ -26,6 +26,7 @@ import jalview.datamodel.Sequence; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; import jalview.io.IdentifyFile; +import jalview.io.NewickFile; import jalview.io.TCoffeeScoreFile; import jalview.schemes.TCoffeeColourScheme; import jalview.util.MessageManager; @@ -142,149 +143,194 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, if (pdbImport) { - PDBEntry pdb = new PDBEntry(); - pdb.setFile(text); + openPdbViewer(text); - if (alignFrame.alignPanel.av.applet.jmolAvailable) - { - new jalview.appletgui.AppletJmol(pdb, new Sequence[] - { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE); - } - else + } + else if (treeImport) + { + if (!loadTree()) { - new MCview.AppletPDBViewer(pdb, new Sequence[] - { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE); + return; } + } + else if (annotationImport) + { + loadAnnotations(); + } + else if (alignFrame != null) + { + loadAlignment(text, newWindow); + } + // TODO: dialog should indicate if data was parsed correctly or not - see + // JAL-1102 + if (this.getParent() instanceof Frame) + { + ((Frame) this.getParent()).setVisible(false); } - else if (treeImport) + else { - try - { - jalview.io.NewickFile fin = new jalview.io.NewickFile( - textarea.getText(), "Paste"); + ((Dialog) this.getParent()).setVisible(false); + } + } - fin.parse(); - if (fin.getTree() != null) - { - alignFrame.loadTree(fin, "Pasted tree file"); - } + /** + * Parses text as Newick Tree format, and loads on to the alignment. Returns + * true if successful, else false. + */ + protected boolean loadTree() + { + try + { + NewickFile fin = new NewickFile(textarea.getText(), "Paste"); - } catch (Exception ex) + fin.parse(); + if (fin.getTree() != null) { - // TODO: JAL-1102 - should have a warning message in dialog, not simply - // overwrite the broken input data with the exception - textarea.setText(MessageManager.formatMessage( - "label.could_not_parse_newick_file", new String[] - { ex.getMessage() })); - return; + alignFrame.loadTree(fin, "Pasted tree file"); + return true; } + } catch (Exception ex) + { + // TODO: JAL-1102 - should have a warning message in dialog, not simply + // overwrite the broken input data with the exception + textarea.setText(MessageManager.formatMessage( + "label.could_not_parse_newick_file", new Object[] + { ex.getMessage() })); + return false; } - else if (annotationImport) + return false; + } + + /** + * Parse text as an alignment file and add to the current or a new window. + * + * @param text + * @param newWindow + */ + protected void loadAlignment(String text, boolean newWindow) + { + Alignment al = null; + + String format = new IdentifyFile().Identify(text, + AppletFormatAdapter.PASTE); + try + { + al = new AppletFormatAdapter().readFile(text, + AppletFormatAdapter.PASTE, format); + } catch (java.io.IOException ex) + { + ex.printStackTrace(); + } + + if (al != null) { - TCoffeeScoreFile tcf = null; - try + al.setDataset(null); + if (newWindow) { - tcf = new TCoffeeScoreFile(textarea.getText(), - jalview.io.AppletFormatAdapter.PASTE); - if (tcf.isValid()) - { - if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), - true)) - { - alignFrame.tcoffeeColour.setEnabled(true); - alignFrame.alignPanel.fontChanged(); - alignFrame.changeColour(new TCoffeeColourScheme( - alignFrame.viewport.getAlignment())); - alignFrame.statusBar - .setText(MessageManager - .getString("label.successfully_pasted_tcoffee_scores_to_alignment")); - } - else - { - // file valid but didn't get added to alignment for some reason - alignFrame.statusBar.setText(MessageManager.formatMessage( - "label.failed_add_tcoffee_scores", - new String[] - { (tcf.getWarningMessage() != null ? tcf - .getWarningMessage() : "") })); - } - } - else - { - tcf = null; - } - } catch (Exception x) + AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet, + "Cut & Paste input - " + format, false); + af.statusBar + .setText(MessageManager + .getString("label.successfully_pasted_annotation_to_alignment")); + } + else { - tcf = null; + alignFrame.addSequences(al.getSequencesArray()); + alignFrame.statusBar.setText(MessageManager + .getString("label.successfully_pasted_alignment_file")); } - if (tcf == null) + } + } + + /** + * Parse the text as a TCoffee score file, if successful add scores as + * alignment annotations. + */ + protected void loadAnnotations() + { + TCoffeeScoreFile tcf = null; + try + { + tcf = new TCoffeeScoreFile(textarea.getText(), + jalview.io.AppletFormatAdapter.PASTE); + if (tcf.isValid()) { - if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport, - textarea.getText(), - jalview.io.AppletFormatAdapter.PASTE)) + if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), + true)) { + alignFrame.tcoffeeColour.setEnabled(true); alignFrame.alignPanel.fontChanged(); - alignFrame.alignPanel.setScrollValues(0, 0); + alignFrame.changeColour(new TCoffeeColourScheme( + alignFrame.viewport.getAlignment())); alignFrame.statusBar .setText(MessageManager - .getString("label.successfully_pasted_annotation_to_alignment")); - + .getString("label.successfully_pasted_tcoffee_scores_to_alignment")); } else { - if (!alignFrame.parseFeaturesFile(textarea.getText(), - jalview.io.AppletFormatAdapter.PASTE)) - { - alignFrame.statusBar - .setText(MessageManager - .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file")); - } + // file valid but didn't get added to alignment for some reason + alignFrame.statusBar.setText(MessageManager.formatMessage( + "label.failed_add_tcoffee_scores", + new Object[] + { (tcf.getWarningMessage() != null ? tcf + .getWarningMessage() : "") })); } } + else + { + tcf = null; + } + } catch (Exception x) + { + tcf = null; } - else if (alignFrame != null) + if (tcf == null) { - Alignment al = null; - - String format = new IdentifyFile().Identify(text, - AppletFormatAdapter.PASTE); - try - { - al = new AppletFormatAdapter().readFile(text, - AppletFormatAdapter.PASTE, format); - } catch (java.io.IOException ex) + if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport, + textarea.getText(), + jalview.io.AppletFormatAdapter.PASTE)) { - ex.printStackTrace(); - } + alignFrame.alignPanel.fontChanged(); + alignFrame.alignPanel.setScrollValues(0, 0); + alignFrame.statusBar + .setText(MessageManager + .getString("label.successfully_pasted_annotation_to_alignment")); - if (al != null) + } + else { - if (newWindow) + if (!alignFrame.parseFeaturesFile(textarea.getText(), + jalview.io.AppletFormatAdapter.PASTE)) { - AlignFrame af = new AlignFrame(al, alignFrame.viewport.applet, - "Cut & Paste input - " + format, false); - af.statusBar + alignFrame.statusBar .setText(MessageManager - .getString("label.successfully_pasted_annotation_to_alignment")); - } - else - { - alignFrame.addSequences(al.getSequencesArray()); - alignFrame.statusBar.setText(MessageManager - .getString("label.successfully_pasted_alignment_file")); + .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file")); } } } - // TODO: dialog should indicate if data was parsed correctly or not - see - // JAL-1102 - if (this.getParent() instanceof Frame) + } + + /** + * Open a Jmol viewer (if available), failing that the built-in PDB viewer, + * passing the input text as the PDB file data. + * + * @param text + */ + protected void openPdbViewer(String text) + { + PDBEntry pdb = new PDBEntry(); + pdb.setFile(text); + + if (alignFrame.alignPanel.av.applet.jmolAvailable) { - ((Frame) this.getParent()).setVisible(false); + new jalview.appletgui.AppletJmol(pdb, new Sequence[] + { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE); } else { - ((Dialog) this.getParent()).setVisible(false); + new MCview.AppletPDBViewer(pdb, new Sequence[] + { seq }, null, alignFrame.alignPanel, AppletFormatAdapter.PASTE); } } diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 1479d94..78853c7 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -327,13 +327,26 @@ public class Sequence implements SequenceI } /** - * DOCUMENT ME! + * Returns the sequence features (if any), looking first on the sequence, then + * on its dataset sequence, and so on until a non-null value is found (or + * none). This supports retrieval of sequence features stored on the sequence + * (as in the applet) or on the dataset sequence (as in the Desktop version). * - * @return DOCUMENT ME! + * @return */ public SequenceFeature[] getSequenceFeatures() { - return sequenceFeatures; + SequenceFeature[] features = sequenceFeatures; + + SequenceI seq = this; + int count = 0; // failsafe against loop in sequence.datasetsequence... + while (features == null && seq.getDatasetSequence() != null + && count++ < 10) + { + seq = seq.getDatasetSequence(); + features = ((Sequence) seq).sequenceFeatures; + } + return features; } public void addPDBId(PDBEntry entry) diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index 5e6ac29..fa91342 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -188,12 +188,11 @@ public class FeatureRenderer extends return initialCol; } - final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq - .getDatasetSequence() : seq; + SequenceFeature[] sf = seq.getSequenceFeatures(); if (seq != lastSeq) { lastSeq = seq; - sequenceFeatures = aseq.getSequenceFeatures(); + sequenceFeatures = sf; if (sequenceFeatures != null) { sfSize = sequenceFeatures.length; @@ -201,9 +200,9 @@ public class FeatureRenderer extends } else { - if (sequenceFeatures != aseq.getSequenceFeatures()) + if (sequenceFeatures != sf) { - sequenceFeatures = aseq.getSequenceFeatures(); + sequenceFeatures = sf; if (sequenceFeatures != null) { sfSize = sequenceFeatures.length; @@ -268,10 +267,8 @@ public class FeatureRenderer extends public synchronized void drawSequence(Graphics g, final SequenceI seq, int start, int end, int y1) { - final SequenceI aseq = (seq.getDatasetSequence() != null) ? seq - .getDatasetSequence() : seq; - if (aseq.getSequenceFeatures() == null - || aseq.getSequenceFeatures().length == 0) + SequenceFeature[] sf = seq.getSequenceFeatures(); + if (sf == null || sf.length == 0) { return; } @@ -284,10 +281,10 @@ public class FeatureRenderer extends updateFeatures(); if (lastSeq == null || seq != lastSeq - || aseq.getSequenceFeatures() != sequenceFeatures) + || sf != sequenceFeatures) { lastSeq = seq; - sequenceFeatures = aseq.getSequenceFeatures(); + sequenceFeatures = sf; } if (transparency != 1 && g != null) diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java index c7cee04..8c2f0da 100644 --- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java +++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java @@ -329,9 +329,7 @@ public abstract class FeatureRendererModel implements for (int i = 0; i < alignment.getHeight(); i++) { SequenceI asq = alignment.getSequenceAt(i); - SequenceI dasq = asq.getDatasetSequence(); - SequenceFeature[] features = dasq != null ? dasq - .getSequenceFeatures() : asq.getSequenceFeatures(); + SequenceFeature[] features = asq.getSequenceFeatures(); if (features == null) { -- 1.7.10.2