X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FCutAndPasteTransfer.java;h=22a49cd7337551ede8f0733df0369f403c89589f;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=bbaeb68cb9ad974e2497e64fdf26c63718f6a088;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java index bbaeb68..22a49cd 100644 --- a/src/jalview/appletgui/CutAndPasteTransfer.java +++ b/src/jalview/appletgui/CutAndPasteTransfer.java @@ -25,12 +25,14 @@ import jalview.api.ComplexAlignFile; import jalview.api.FeaturesSourceI; import jalview.bin.JalviewLite; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.io.AlignmentFileReaderI; import jalview.io.AnnotationFile; import jalview.io.AppletFormatAdapter; -import jalview.io.FileParse; +import jalview.io.DataSourceType; +import jalview.io.FileFormatI; import jalview.io.IdentifyFile; import jalview.io.NewickFile; import jalview.io.TCoffeeScoreFile; @@ -51,9 +53,10 @@ import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; +import java.io.IOException; -public class CutAndPasteTransfer extends Panel implements ActionListener, - MouseListener +public class CutAndPasteTransfer extends Panel + implements ActionListener, MouseListener { boolean pdbImport = false; @@ -65,7 +68,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, AlignFrame alignFrame; - FileParse source = null; + AlignmentFileReaderI source = null; public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame) { @@ -194,7 +197,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, { try { - NewickFile fin = new NewickFile(textarea.getText(), "Paste"); + NewickFile fin = new NewickFile(textarea.getText(), + DataSourceType.PASTE); fin.parse(); if (fin.getTree() != null) @@ -207,8 +211,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, // 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() })); + "label.could_not_parse_newick_file", new Object[] + { ex.getMessage() })); return false; } return false; @@ -225,76 +229,76 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, { AlignmentI al = null; - String format = new IdentifyFile().identify(text, - AppletFormatAdapter.PASTE); - AppletFormatAdapter afa = new AppletFormatAdapter(alignFrame.alignPanel); try { - al = afa.readFile(text, AppletFormatAdapter.PASTE, format); + FileFormatI format = new IdentifyFile().identify(text, + DataSourceType.PASTE); + AppletFormatAdapter afa = new AppletFormatAdapter( + alignFrame.alignPanel); + al = afa.readFile(text, DataSourceType.PASTE, format); source = afa.getAlignFile(); - } catch (java.io.IOException ex) - { - ex.printStackTrace(); - } - if (al != null) - { - al.setDataset(null); // set dataset on alignment/sequences - - /* - * SplitFrame option dependent on applet parameter for now. - */ - boolean allowSplitFrame = alignFrame.viewport.applet - .getDefaultParameter("enableSplitFrame", false); - if (allowSplitFrame && openSplitFrame(al, format)) + if (al != null) { - return; - } - if (newWindow) - { - AlignFrame af; - - if (source instanceof ComplexAlignFile) + al.setDataset(null); // set dataset on alignment/sequences + + /* + * SplitFrame option dependent on applet parameter for now. + */ + boolean allowSplitFrame = alignFrame.viewport.applet + .getDefaultParameter("enableSplitFrame", false); + if (allowSplitFrame && openSplitFrame(al, format)) { - ColumnSelection colSel = ((ComplexAlignFile) source) - .getColumnSelection(); - SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) - .getHiddenSequences(); - boolean showSeqFeatures = ((ComplexAlignFile) source) - .isShowSeqFeatures(); - String colourSchemeName = ((ComplexAlignFile) source) - .getGlobalColourScheme(); - af = new AlignFrame(al, hiddenSeqs, colSel, - alignFrame.viewport.applet, "Cut & Paste input - " - + format, false); - af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures); - ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( - colourSchemeName, al); - if (cs != null) + return; + } + if (newWindow) + { + AlignFrame af; + + if (source instanceof ComplexAlignFile) { - af.changeColour(cs); + HiddenColumns colSel = ((ComplexAlignFile) source) + .getHiddenColumns(); + SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) + .getHiddenSequences(); + boolean showSeqFeatures = ((ComplexAlignFile) source) + .isShowSeqFeatures(); + String colourSchemeName = ((ComplexAlignFile) source) + .getGlobalColourScheme(); + af = new AlignFrame(al, hiddenSeqs, colSel, + alignFrame.viewport.applet, + "Cut & Paste input - " + format, false); + af.getAlignViewport().setShowSequenceFeatures(showSeqFeatures); + ColourSchemeI cs = ColourSchemeMapper + .getJalviewColourScheme(colourSchemeName, al); + if (cs != null) + { + af.changeColour(cs); + } } + else + { + af = new AlignFrame(al, alignFrame.viewport.applet, + "Cut & Paste input - " + format, false); + if (source instanceof FeaturesSourceI) + { + af.getAlignViewport().setShowSequenceFeatures(true); + } + } + + af.statusBar.setText(MessageManager.getString( + "label.successfully_pasted_annotation_to_alignment")); } else { - af = new AlignFrame(al, alignFrame.viewport.applet, - "Cut & Paste input - " + format, false); - if (source instanceof FeaturesSourceI) - { - af.getAlignViewport().setShowSequenceFeatures(true); - } + alignFrame.addSequences(al.getSequencesArray()); + alignFrame.statusBar.setText(MessageManager + .getString("label.successfully_pasted_alignment_file")); } - - af.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")); } + } catch (IOException ex) + { + ex.printStackTrace(); } } @@ -306,7 +310,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, * @param al * @return */ - protected boolean openSplitFrame(AlignmentI al, String format) + protected boolean openSplitFrame(AlignmentI al, FileFormatI format) { final AlignmentI thisAlignment = this.alignFrame.getAlignViewport() .getAlignment(); @@ -376,7 +380,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, try { tcf = new TCoffeeScoreFile(textarea.getText(), - jalview.io.AppletFormatAdapter.PASTE); + jalview.io.DataSourceType.PASTE); if (tcf.isValid()) { if (tcf.annotateAlignment(alignFrame.viewport.getAlignment(), true)) @@ -385,17 +389,17 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, alignFrame.alignPanel.fontChanged(); alignFrame.changeColour(new TCoffeeColourScheme( alignFrame.viewport.getAlignment())); - alignFrame.statusBar - .setText(MessageManager - .getString("label.successfully_pasted_tcoffee_scores_to_alignment")); + 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 Object[] { (tcf.getWarningMessage() != null ? tcf - .getWarningMessage() : "") })); + "label.failed_add_tcoffee_scores", new Object[] + { (tcf.getWarningMessage() != null + ? tcf.getWarningMessage() + : "") })); } } else @@ -409,23 +413,21 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, if (tcf == null) { if (new AnnotationFile().annotateAlignmentView(alignFrame.viewport, - textarea.getText(), jalview.io.AppletFormatAdapter.PASTE)) + textarea.getText(), jalview.io.DataSourceType.PASTE)) { alignFrame.alignPanel.fontChanged(); alignFrame.alignPanel.setScrollValues(0, 0); - alignFrame.statusBar - .setText(MessageManager - .getString("label.successfully_pasted_annotation_to_alignment")); + alignFrame.statusBar.setText(MessageManager.getString( + "label.successfully_pasted_annotation_to_alignment")); } else { if (!alignFrame.parseFeaturesFile(textarea.getText(), - jalview.io.AppletFormatAdapter.PASTE)) + jalview.io.DataSourceType.PASTE)) { - alignFrame.statusBar - .setText(MessageManager - .getString("label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file")); + alignFrame.statusBar.setText(MessageManager.getString( + "label.couldnt_parse_pasted_text_as_valid_annotation_feature_GFF_tcoffee_file")); } } } @@ -445,12 +447,12 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, if (alignFrame.alignPanel.av.applet.jmolAvailable) { new jalview.appletgui.AppletJmol(pdb, new SequenceI[] { seq }, null, - alignFrame.alignPanel, AppletFormatAdapter.PASTE); + alignFrame.alignPanel, DataSourceType.PASTE); } else { new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null, - alignFrame.alignPanel, AppletFormatAdapter.PASTE); + alignFrame.alignPanel, DataSourceType.PASTE); } } @@ -482,8 +484,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, private void jbInit() throws Exception { textarea.setFont(new java.awt.Font("Monospaced", Font.PLAIN, 10)); - textarea.setText(MessageManager - .getString("label.paste_your_alignment_file")); + textarea.setText( + MessageManager.getString("label.paste_your_alignment_file")); textarea.addMouseListener(this); this.setLayout(borderLayout1); accept.addActionListener(this); @@ -499,8 +501,8 @@ public class CutAndPasteTransfer extends Panel implements ActionListener, @Override public void mousePressed(MouseEvent evt) { - if (textarea.getText().startsWith( - MessageManager.getString("label.paste_your"))) + if (textarea.getText() + .startsWith(MessageManager.getString("label.paste_your"))) { textarea.setText(""); }