X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;fp=src%2Fjalview%2Fio%2FFileLoader.java;h=4f83ab1235e14be8b9879f6797f55d70cd7dceff;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=b449d19aba7692a4481264805f97c784584dd8f1;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index b449d19..4f83ab1 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -24,6 +24,7 @@ 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; @@ -33,6 +34,7 @@ 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; @@ -41,18 +43,18 @@ 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 + AlignmentFileReaderI source = null; // alternative specification of where data + // comes // from @@ -86,13 +88,14 @@ 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; @@ -116,7 +119,7 @@ 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); } @@ -125,27 +128,28 @@ 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(); } @@ -157,12 +161,13 @@ public class FileLoader implements Runnable * @param format * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format) + public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source, + FileFormatI format) { this.source = source; file = source.getInFile(); - protocol = source.type; + protocol = source.getDataSourceType(); this.format = format; return _LoadFileWaitTillLoaded(); } @@ -194,13 +199,13 @@ 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); @@ -229,18 +234,18 @@ 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.getName()); } } @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 @@ -254,10 +259,8 @@ 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 { @@ -266,20 +269,20 @@ public class FileLoader implements Runnable } - if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE")) + if (format == null) { Desktop.instance.stopLoading(); System.err.println("The input file \"" + file + "\" has null or unidentifiable data content!"); if (!Jalview.isHeadlessMode()) { - javax.swing.JOptionPane.showInternalMessageDialog( + JvOptionPane.showInternalMessageDialog( Desktop.desktop, MessageManager.getString("label.couldnt_read_data") + " in " + file + "\n" - + AppletFormatAdapter.SUPPORTED_FORMATS, + + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } return; } @@ -296,7 +299,7 @@ public class FileLoader implements Runnable loadtime = -System.currentTimeMillis(); AlignmentI al = null; - if (format.equalsIgnoreCase("Jalview")) + if (FileFormat.Jalview.equals(format)) { if (source != null) { @@ -309,37 +312,26 @@ public class FileLoader implements Runnable } else { - String error = AppletFormatAdapter.SUPPORTED_FORMATS; - if (FormatAdapter.isValidFormat(format)) + String error = AppletFormatAdapter.getSupportedFormats(); + try { - try + if (source != null) { - if (source != null) - { - // read from the provided source - al = new FormatAdapter().readFromFile(source, format); - } - else - { - - // open a new source and read from it - FormatAdapter fa = new FormatAdapter(); - al = fa.readFile(file, protocol, format); - source = fa.getAlignFile(); // keep reference for later if - // necessary. - } - } catch (java.io.IOException ex) - { - error = ex.getMessage(); + // read from the provided source + al = new FormatAdapter().readFromFile(source, format); } - } - else - { - if (format != null && format.length() > 7) + else { - // ad hoc message in format. - error = format + "\n" + error; + + // open a new source and read from it + FormatAdapter fa = new FormatAdapter(); + al = fa.readFile(file, protocol, format); + source = fa.getAlignFile(); // keep reference for later if + // necessary. } + } catch (java.io.IOException ex) + { + error = ex.getMessage(); } if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence()) @@ -410,7 +402,7 @@ public class FileLoader implements Runnable } } // add metadata and update ui - if (!protocol.equals(AppletFormatAdapter.PASTE)) + if (!(protocol == DataSourceType.PASTE)) { alignFrame.setFileName(file, format); } @@ -464,10 +456,10 @@ public class FileLoader implements 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); } }); } @@ -491,12 +483,12 @@ public class FileLoader implements Runnable @Override public void run() { - javax.swing.JOptionPane.showInternalMessageDialog( + JvOptionPane.showInternalMessageDialog( Desktop.desktop, MessageManager.formatMessage( "label.problems_opening_file", new String[] { file }), MessageManager .getString("label.file_open_error"), - javax.swing.JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -513,12 +505,12 @@ public class FileLoader implements 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); } }); }