X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=3644b28691d0fddff130add1c80773c72656cf4c;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=7b751bf436bc9f17791ef6188221c982c2d40fe0;hpb=fee1b781ca14aadea5d112fc554fe14879c787c5;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 7b751bf..3644b28 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -63,10 +63,14 @@ import jalview.gui.ViewSelectionMenu.ViewSetProvider; import jalview.io.AlignmentProperties; import jalview.io.AnnotationFile; import jalview.io.BioJsHTMLOutput; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.io.FileFormatI; import jalview.io.FileLoader; import jalview.io.FormatAdapter; import jalview.io.HtmlSvgOutput; import jalview.io.IdentifyFile; +import jalview.io.JPredFile; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.JnetAnnotationMaker; @@ -176,7 +180,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Last format used to load or save alignments in this window */ - String currentFileFormat = null; + FileFormatI currentFileFormat = null; /** * Current filename for this alignment @@ -485,7 +489,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param format * format of file */ - public void setFileName(String file, String format) + public void setFileName(String file, FileFormatI format) { fileName = file; setFileFormat(format); @@ -1014,7 +1018,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // originating file's format // TODO: work out how to recover feature settings for correct view(s) when // file is reloaded. - if (currentFileFormat.equals("Jalview")) + if (FileFormat.Jalview.equals(currentFileFormat)) { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int i = 0; i < frames.length; i++) @@ -1036,7 +1040,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance.closeAssociatedWindows(); FileLoader loader = new FileLoader(); - String protocol = fileName.startsWith("http:") ? "URL" : "File"; + DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL + : DataSourceType.FILE; loader.LoadFile(viewport, fileName, protocol, currentFileFormat); } else @@ -1044,7 +1049,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Rectangle bounds = this.getBounds(); FileLoader loader = new FileLoader(); - String protocol = fileName.startsWith("http:") ? "URL" : "File"; + DataSourceType protocol = fileName.startsWith("http:") ? DataSourceType.URL + : DataSourceType.FILE; AlignFrame newframe = loader.LoadFileWaitTillLoaded(fileName, protocol, currentFileFormat); @@ -1088,9 +1094,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void save_actionPerformed(ActionEvent e) { - if (fileName == null - || (currentFileFormat == null || !jalview.io.FormatAdapter - .isValidIOFormat(currentFileFormat, true)) + if (fileName == null || (currentFileFormat == null) || fileName.startsWith("http")) { saveAs_actionPerformed(null); @@ -1110,11 +1114,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void saveAs_actionPerformed(ActionEvent e) { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY"), - jalview.io.AppletFormatAdapter.WRITABLE_EXTENSIONS, - jalview.io.AppletFormatAdapter.WRITABLE_FNAMES, - currentFileFormat, false); + JalviewFileChooser chooser = JalviewFileChooser.forWrite( + Cache.getProperty("LAST_DIRECTORY"), + // AppletFormatAdapter.WRITABLE_EXTENSIONS, + // AppletFormatAdapter.WRITABLE_FNAMES, + currentFileFormat.toString(), false); chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle(MessageManager @@ -1146,24 +1150,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fileName = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", - currentFileFormat); + Cache.setProperty("DEFAULT_FILE_FORMAT", + currentFileFormat.toString()); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName); - if (currentFileFormat.indexOf(" ") > -1) - { - currentFileFormat = currentFileFormat.substring(0, - currentFileFormat.indexOf(" ")); - } + Cache.setProperty("LAST_DIRECTORY", fileName); saveAlignment(fileName, currentFileFormat); } } - public boolean saveAlignment(String file, String format) + public boolean saveAlignment(String file, FileFormatI format) { boolean success = true; - if (format.equalsIgnoreCase("Jalview")) + if (FileFormat.Jalview.equals(format)) { String shortName = title; @@ -1182,16 +1181,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } else { - if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) - { - warningMessage("Cannot save file " + fileName + " using format " - + format, "Alignment output format not supported"); - if (!Jalview.isHeadlessMode()) - { - saveAs_actionPerformed(null); - } - return false; - } + // if (!jalview.io.AppletFormatAdapter.isValidFormat(format, true)) + // { + // warningMessage("Cannot save file " + fileName + " using format " + // + format, "Alignment output format not supported"); + // if (!Jalview.isHeadlessMode()) + // { + // saveAs_actionPerformed(null); + // } + // return false; + // } AlignmentExportData exportData = getAlignmentForExport(format, viewport, null); @@ -1271,8 +1270,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, protected void outputText_actionPerformed(ActionEvent e) { - AlignmentExportData exportData = getAlignmentForExport( - e.getActionCommand(), viewport, null); + FileFormatI fileFormat = FileFormat.forName(e.getActionCommand()); + AlignmentExportData exportData = getAlignmentForExport(fileFormat, + viewport, null); if (exportData.getSettings().isCancelled()) { return; @@ -1281,8 +1281,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cap.setForInput(null); try { + FileFormatI format = fileFormat; cap.setText(new FormatAdapter(alignPanel, exportData.getSettings()) - .formatSequences(e.getActionCommand(), + .formatSequences(format, exportData.getAlignment(), exportData.getOmitHidden(), exportData.getStartEndPostions(), @@ -1299,7 +1300,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } public static AlignmentExportData getAlignmentForExport( - String exportFormat, AlignViewportI viewport, + FileFormatI format, AlignViewportI viewport, AlignExportSettingI exportSettings) { AlignmentI alignmentToExport = null; @@ -1315,7 +1316,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (settings == null) { settings = new AlignExportSettings(hasHiddenSeqs, - viewport.hasHiddenColumns(), exportFormat); + viewport.hasHiddenColumns(), format); } // settings.isExportAnnotations(); @@ -1873,7 +1874,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, omitHidden = viewport.getViewAsString(true); } - String output = new FormatAdapter().formatSequences("Fasta", seqs, + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, null); StringSelection ss = new StringSelection(output); @@ -1960,7 +1962,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - String str, format; + String str; + FileFormatI format; try { str = (String) contents.getTransferData(DataFlavor.stringFlavor); @@ -1969,7 +1972,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - format = new IdentifyFile().identify(str, "Paste"); + format = new IdentifyFile().identify(str, DataSourceType.PASTE); } catch (OutOfMemoryError er) { @@ -1999,7 +2002,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, else { // parse the clipboard as an alignment. - alignment = new FormatAdapter().readFile(str, "Paste", format); + alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE, + format); sequences = alignment.getSequencesArray(); } @@ -4326,7 +4330,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jalview.io.NewickFile fin = null; try { - fin = new jalview.io.NewickFile(choice, "File"); + fin = new NewickFile(choice, DataSourceType.FILE); viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree()); } catch (Exception ex) { @@ -4766,11 +4770,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Set the file format * - * @param fileFormat + * @param format */ - public void setFileFormat(String fileFormat) + public void setFileFormat(FileFormatI format) { - this.currentFileFormat = fileFormat; + this.currentFileFormat = format; } /** @@ -4778,14 +4782,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * * @param file * contents or path to retrieve file - * @param type + * @param sourceType * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed correctly. */ - public boolean parseFeaturesFile(String file, String type) + public boolean parseFeaturesFile(String file, DataSourceType sourceType) { - return avc.parseFeaturesFile(file, type, - jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false)); + return avc.parseFeaturesFile(file, sourceType, + Cache.getDefault("RELAXEDSEQIDMATCHING", false)); } @@ -4830,7 +4834,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Java's Transferable for native dnd evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); Transferable t = evt.getTransferable(); - java.util.List files = new ArrayList(), protocols = new ArrayList(); + List files = new ArrayList(); + List protocols = new ArrayList(); try { @@ -4856,13 +4861,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { String file = files.get(i).toString(); String pdbfn = ""; - String protocol = FormatAdapter.checkProtocol(file); - if (protocol == jalview.io.FormatAdapter.FILE) + DataSourceType protocol = FormatAdapter.checkProtocol(file); + if (protocol == DataSourceType.FILE) { File fl = new File(file); pdbfn = fl.getName(); } - else if (protocol == jalview.io.FormatAdapter.URL) + else if (protocol == DataSourceType.URL) { URL url = new URL(file); pdbfn = url.getFile(); @@ -4886,7 +4891,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (mtch != null) { - String type = null; + FileFormatI type = null; try { type = new IdentifyFile().identify(file, protocol); @@ -4896,7 +4901,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (type != null) { - if (StructureFile.isStructureFile(type)) + if (FileFormat.PDB.equals(type) || FileFormat.MMCif.equals(type)) { filesmatched.add(new Object[] { file, protocol, mtch }); continue; @@ -4936,7 +4941,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { PDBEntry pe = new AssociatePdbFileWithSeq() .associatePdbWithSeq((String) fm[0], - (String) fm[1], toassoc, false, + (DataSourceType) fm[1], toassoc, false, Desktop.instance); if (pe != null) { @@ -4995,21 +5000,21 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * @param file * either a filename or a URL string. */ - public void loadJalviewDataFile(String file, String protocol, - String format, SequenceI assocSeq) + public void loadJalviewDataFile(String file, DataSourceType sourceType, + FileFormatI format, SequenceI assocSeq) { try { - if (protocol == null) + if (sourceType == null) { - protocol = FormatAdapter.checkProtocol(file); + sourceType = FormatAdapter.checkProtocol(file); } // if the file isn't identified, or not positively identified as some // other filetype (PFAM is default unidentified alignment file type) then // try to parse as annotation. - boolean isAnnotation = (format == null || format - .equalsIgnoreCase("PFAM")) ? new AnnotationFile() - .annotateAlignmentView(viewport, file, protocol) : false; + boolean isAnnotation = (format == null || FileFormat.Pfam + .equals(format)) ? new AnnotationFile() + .annotateAlignmentView(viewport, file, sourceType) : false; if (!isAnnotation) { @@ -5017,7 +5022,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, TCoffeeScoreFile tcf = null; try { - tcf = new TCoffeeScoreFile(file, protocol); + tcf = new TCoffeeScoreFile(file, sourceType); if (tcf.isValid()) { if (tcf.annotateAlignment(viewport.getAlignment(), true)) @@ -5063,12 +5068,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // try to parse it as a features file if (format == null) { - format = new IdentifyFile().identify(file, protocol); + format = new IdentifyFile().identify(file, sourceType); } - if (format.equalsIgnoreCase("JnetFile")) + if (FileFormat.Jnet.equals(format)) { - jalview.io.JPredFile predictions = new jalview.io.JPredFile( - file, protocol); + JPredFile predictions = new JPredFile( + file, sourceType); new JnetAnnotationMaker(); JnetAnnotationMaker.add_annotation(predictions, viewport.getAlignment(), 0, false); @@ -5079,16 +5084,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.setColumnSelection(cs); isAnnotation = true; } - else if (IdentifyFile.FeaturesFile.equals(format)) + // else if (IdentifyFile.FeaturesFile.equals(format)) + else if (FileFormat.Features.equals(format)) { - if (parseFeaturesFile(file, protocol)) + if (parseFeaturesFile(file, sourceType)) { alignPanel.paintAlignment(true); } } else { - new FileLoader().LoadFile(viewport, file, protocol, format); + new FileLoader().LoadFile(viewport, file, sourceType, format); } } } @@ -5113,8 +5119,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } new OOMWarning( "loading data " - + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard." - : "using " + protocol + " from " + file) + + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard." + : "using " + sourceType + " from " + file) : ".") + (format != null ? "(parsing as '" + format + "' file)" : ""), oom, Desktop.desktop);