X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=3ad74c71ff2bed320f08579b9f1081459f15751f;hb=3a83e3b795ee674956d0ce18b9a89a825f7b5a8e;hp=18ab642be987901d19a54679c0f5ba8e98ec774f;hpb=3f3c6c3a2b99fee2e726d18302af1b3320331212;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 18ab642..3ad74c7 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -21,7 +21,11 @@ package jalview.io; import jalview.api.ComplexAlignFile; +import jalview.api.FeatureSettingsModelI; import jalview.api.FeaturesDisplayedI; +import jalview.api.FeaturesSourceI; +import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; @@ -30,6 +34,8 @@ import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; import jalview.gui.Desktop; import jalview.gui.Jalview2XML; +import jalview.gui.JvOptionPane; +import jalview.json.binding.biojson.v1.ColourSchemeMapper; import jalview.schemes.ColourSchemeI; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; @@ -37,18 +43,17 @@ import jalview.util.MessageManager; import java.util.StringTokenizer; import java.util.Vector; -import javax.swing.JOptionPane; import javax.swing.SwingUtilities; public class FileLoader implements Runnable { String file; - String protocol; + DataSourceType protocol; - String format; + FileFormatI format; - FileParse source = null; // alternative specification of where data comes + AlignmentFileI source = null; // alternative specification of where data comes // from @@ -82,13 +87,14 @@ public class FileLoader implements Runnable } public void LoadFile(AlignViewport viewport, String file, - String protocol, String format) + DataSourceType protocol, FileFormatI format) { this.viewport = viewport; LoadFile(file, protocol, format); } - public void LoadFile(String file, String protocol, String format) + public void LoadFile(String file, DataSourceType protocol, + FileFormatI format) { this.file = file; this.protocol = protocol; @@ -98,6 +104,7 @@ public class FileLoader implements Runnable SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { loader.start(); @@ -111,7 +118,7 @@ public class FileLoader implements Runnable * @param file * @param protocol */ - public void LoadFile(String file, String protocol) + public void LoadFile(String file, DataSourceType protocol) { LoadFile(file, protocol, null); } @@ -120,27 +127,28 @@ public class FileLoader implements Runnable * Load alignment from (file, protocol) and wait till loaded * * @param file - * @param protocol + * @param sourceType * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(String file, String protocol) + public AlignFrame LoadFileWaitTillLoaded(String file, + DataSourceType sourceType) { - return LoadFileWaitTillLoaded(file, protocol, null); + return LoadFileWaitTillLoaded(file, sourceType, null); } /** * Load alignment from (file, protocol) of type format and wait till loaded * * @param file - * @param protocol + * @param sourceType * @param format * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, - String format) + public AlignFrame LoadFileWaitTillLoaded(String file, + DataSourceType sourceType, FileFormatI format) { this.file = file; - this.protocol = protocol; + this.protocol = sourceType; this.format = format; return _LoadFileWaitTillLoaded(); } @@ -152,12 +160,13 @@ public class FileLoader implements Runnable * @param format * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format) + public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source, + FileFormatI format) { this.source = source; file = source.getInFile(); - protocol = source.type; + protocol = source.getDataSourceType(); this.format = format; return _LoadFileWaitTillLoaded(); } @@ -189,13 +198,13 @@ public class FileLoader implements Runnable public void updateRecentlyOpened() { Vector recent = new Vector(); - if (protocol.equals(FormatAdapter.PASTE)) + if (protocol == DataSourceType.PASTE) { // do nothing if the file was pasted in as text... there is no filename to // refer to it as. return; } - String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE" + String type = protocol == DataSourceType.FILE ? "RECENT_FILE" : "RECENT_URL"; String historyItems = jalview.bin.Cache.getProperty(type); @@ -224,17 +233,18 @@ public class FileLoader implements Runnable newHistory.append(recent.elementAt(i)); } - jalview.bin.Cache.setProperty(type, newHistory.toString()); + Cache.setProperty(type, newHistory.toString()); - if (protocol.equals(FormatAdapter.FILE)) + if (protocol == DataSourceType.FILE) { - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format); + Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString()); } } + @Override public void run() { - String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard" + String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard" : file; Runtime rt = Runtime.getRuntime(); try @@ -248,15 +258,32 @@ public class FileLoader implements Runnable // just in case the caller didn't identify the file for us if (source != null) { - format = new IdentifyFile().Identify(source, false); // identify - // stream and - // rewind rather - // than close + format = new IdentifyFile().identify(source, false); + // identify stream and rewind rather than close } else { - format = new IdentifyFile().Identify(file, protocol); + format = new IdentifyFile().identify(file, protocol); } + + } + + if (format == null) + { + Desktop.instance.stopLoading(); + System.err.println("The input file \"" + file + + "\" has null or unidentifiable data content!"); + if (!Jalview.isHeadlessMode()) + { + JvOptionPane.showInternalMessageDialog( + Desktop.desktop, + MessageManager.getString("label.couldnt_read_data") + + " in " + file + "\n" + + AppletFormatAdapter.SUPPORTED_FORMATS, + MessageManager.getString("label.couldnt_read_data"), + JvOptionPane.WARNING_MESSAGE); + } + return; } // TODO: cache any stream datasources as a temporary file (eg. PDBs // retrieved via URL) @@ -271,7 +298,7 @@ public class FileLoader implements Runnable loadtime = -System.currentTimeMillis(); AlignmentI al = null; - if (format.equalsIgnoreCase("Jalview")) + if (FileFormat.Jalview.equals(format)) { if (source != null) { @@ -285,14 +312,12 @@ public class FileLoader implements Runnable else { String error = AppletFormatAdapter.SUPPORTED_FORMATS; - if (FormatAdapter.isValidFormat(format)) - { try { if (source != null) { // read from the provided source - al = new FormatAdapter().readFromFile(source, format); + al = new FormatAdapter().readFromFile(source, format); } else { @@ -307,17 +332,8 @@ public class FileLoader implements Runnable { error = ex.getMessage(); } - } - else - { - if (format != null && format.length() > 7) - { - // ad hoc message in format. - error = format + "\n" + error; - } - } - if ((al != null) && (al.getHeight() > 0)) + if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence()) { // construct and register dataset sequences for (SequenceI sq : al.getSequences()) @@ -326,9 +342,9 @@ public class FileLoader implements Runnable { sq = sq.getDatasetSequence(); } - if (sq.getPDBId() != null) + if (sq.getAllPDBEntries() != null) { - for (PDBEntry pdbe : sq.getPDBId()) + for (PDBEntry pdbe : sq.getAllPDBEntries()) { // register PDB entries with desktop's structure selection // manager @@ -338,8 +354,14 @@ public class FileLoader implements Runnable } } + FeatureSettingsModelI proxyColourScheme = source + .getFeatureColourScheme(); if (viewport != null) { + if (proxyColourScheme != null) + { + viewport.applyFeaturesStyle(proxyColourScheme); + } // append to existing alignment viewport.addAlignment(al, title); } @@ -353,34 +375,44 @@ public class FileLoader implements Runnable .getColumnSelection(); SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) .getHiddenSequences(); - boolean showSeqFeatures = ((ComplexAlignFile) source) - .isShowSeqFeatures(); - ColourSchemeI cs = ((ComplexAlignFile) source) - .getColourScheme(); + String colourSchemeName = ((ComplexAlignFile) source) + .getGlobalColourScheme(); FeaturesDisplayedI fd = ((ComplexAlignFile) source) .getDisplayedFeatures(); alignFrame = new AlignFrame(al, hiddenSeqs, colSel, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - - alignFrame.getViewport().setShowSequenceFeatures( - showSeqFeatures); alignFrame.getViewport().setFeaturesDisplayed(fd); - alignFrame.changeColour(cs); + alignFrame.getViewport().setShowSequenceFeatures( + ((ComplexAlignFile) source).isShowSeqFeatures()); + ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( + colourSchemeName, al); + if (cs != null) + { + alignFrame.changeColour(cs); + } } else { alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + if (source instanceof FeaturesSourceI) + { + alignFrame.getViewport().setShowSequenceFeatures(true); + } } // add metadata and update ui - if (!protocol.equals(AppletFormatAdapter.PASTE)) + if (!(protocol == DataSourceType.PASTE)) { alignFrame.setFileName(file, format); } - + if (proxyColourScheme != null) + { + alignFrame.getViewport() + .applyFeaturesStyle(proxyColourScheme); + } alignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", new String[] - { title })); + "label.successfully_loaded_file", + new String[] { title })); if (raiseGUI) { @@ -409,20 +441,24 @@ public class FileLoader implements Runnable Desktop.instance.stopLoading(); } - final String errorMessage = "Couldn't load file " + title + "\n" - + error; + final String errorMessage = MessageManager + .getString("label.couldnt_load_file") + + " " + + title + + "\n" + error; // TODO: refactor FileLoader to be independent of Desktop / Applet GUI // bits ? if (raiseGUI && Desktop.desktop != null) { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, errorMessage, MessageManager .getString("label.error_loading_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -443,14 +479,15 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - javax.swing.JOptionPane.showInternalMessageDialog( + JvOptionPane.showInternalMessageDialog( Desktop.desktop, MessageManager.formatMessage( - "label.problems_opening_file", new String[] - { file }), MessageManager + "label.problems_opening_file", + new String[] { file }), MessageManager .getString("label.file_open_error"), - javax.swing.JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -464,14 +501,15 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - javax.swing.JOptionPane.showInternalMessageDialog( + JvOptionPane.showInternalMessageDialog( Desktop.desktop, MessageManager.formatMessage( "warn.out_of_memory_loading_file", new String[] { file }), MessageManager .getString("label.out_of_memory"), - javax.swing.JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -522,6 +560,7 @@ public class FileLoader implements Runnable * * @see java.lang.Object#finalize() */ + @Override protected void finalize() throws Throwable { source = null;