X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=449c68577b21249f9f4d3ee763b61b3b9e5697b9;hb=a7bc89415a6749ff89eb97f75fbc950a433a4935;hp=dcfdd22ce13be4e1a9b6ec3458b77c452df40eb0;hpb=3516fc4a1037ffc86d51f900850ed7a04a0174cb;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index dcfdd22..449c685 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,6 +20,13 @@ */ package jalview.io; +import java.io.File; +import java.io.IOException; +import java.util.StringTokenizer; +import java.util.Vector; + +import javax.swing.SwingUtilities; + import jalview.api.ComplexAlignFile; import jalview.api.FeatureSettingsModelI; import jalview.api.FeaturesDisplayedI; @@ -33,27 +40,15 @@ import jalview.datamodel.SequenceI; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; import jalview.gui.Desktop; -import jalview.gui.Jalview2XML; import jalview.gui.JvOptionPane; +import jalview.gui.QuitHandler; import jalview.json.binding.biojson.v1.ColourSchemeMapper; +import jalview.project.Jalview2XML; import jalview.schemes.ColourSchemeI; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; import jalview.ws.utils.UrlDownloadClient; -import java.io.BufferedReader; -import java.io.ByteArrayInputStream; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.FileReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.util.StringTokenizer; -import java.util.Vector; - -import javax.swing.SwingUtilities; - public class FileLoader implements Runnable { String file; @@ -102,7 +97,8 @@ public class FileLoader implements Runnable DataSourceType protocol, FileFormatI format) { this.viewport = viewport; - if (file instanceof File) { + if (file instanceof File) + { this.selectedFile = (File) file; file = selectedFile.getPath(); } @@ -214,6 +210,7 @@ public class FileLoader implements Runnable protected AlignFrame _LoadFileWaitTillLoaded() { this.run(); + return alignFrame; } @@ -276,6 +273,7 @@ public class FileLoader implements Runnable ? "Copied From Clipboard" : file; Runtime rt = Runtime.getRuntime(); + try { if (Desktop.instance != null) @@ -290,7 +288,8 @@ public class FileLoader implements Runnable format = new IdentifyFile().identify(source, false); // identify stream and rewind rather than close } - else if (selectedFile != null) { + else if (selectedFile != null) + { format = new IdentifyFile().identify(selectedFile, protocol); } else @@ -314,6 +313,7 @@ public class FileLoader implements Runnable MessageManager.getString("label.couldnt_read_data"), JvOptionPane.WARNING_MESSAGE); } + this.setShouldBeSaved(); return; } // TODO: cache any stream datasources as a temporary file (eg. PDBs @@ -338,7 +338,9 @@ public class FileLoader implements Runnable "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream."); // We read the data anyway - it might make sense. } - alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file); + // BH 2018 switch to File object here instead of filename + alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign( + selectedFile == null ? file : selectedFile); } else { @@ -366,27 +368,29 @@ public class FileLoader implements Runnable file.lastIndexOf(".")); String tempStructureFileStr = createNamedJvTempFile( urlLeafName, structExt); - + // BH - switching to File object here so as to hold // ._bytes array directly File tempFile = new File(tempStructureFileStr); UrlDownloadClient.download(file, tempFile); - - al = fa.readFile(tempFile, DataSourceType.FILE, - format); + + al = fa.readFile(tempFile, DataSourceType.FILE, format); source = fa.getAlignFile(); } else { - if (selectedFile == null) { - al = fa.readFile(file, protocol, format); - - } else { - al = fa.readFile(selectedFile, protocol, format); - } + if (selectedFile == null) + { + al = fa.readFile(null, file, protocol, format); + + } + else + { + al = fa.readFile(selectedFile, null, protocol, format); + } source = fa.getAlignFile(); // keep reference for later if - - // necessary. + + // necessary. } } } catch (java.io.IOException ex) @@ -420,12 +424,9 @@ public class FileLoader implements Runnable .getFeatureColourScheme(); if (viewport != null) { - if (proxyColourScheme != null) - { - viewport.applyFeaturesStyle(proxyColourScheme); - } // append to existing alignment viewport.addAlignment(al, title); + viewport.applyFeaturesStyle(proxyColourScheme); } else { @@ -486,12 +487,18 @@ public class FileLoader implements Runnable // that perform queries to find the 'current working alignment' Desktop.addInternalFrame(alignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + + /* + * for an Overview automatically opened with alignment, + * set its title now alignFrame title has been set + */ + alignFrame.alignPanel.setOverviewTitle(alignFrame); } try { - alignFrame.setMaximum(jalview.bin.Cache - .getDefault("SHOW_FULLSCREEN", false)); + alignFrame.setMaximum( + Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -614,6 +621,7 @@ public class FileLoader implements Runnable Desktop.instance.stopLoading(); } + this.setShouldBeSaved(); } /** @@ -639,21 +647,21 @@ public class FileLoader implements Runnable return tempStructFile.toString(); } - /** - * - * @param file a File, or a String which is a name of a file - * @return - * @throws FileNotFoundException + /* + * set whether quit should ask to save when just loaded this source */ - @SuppressWarnings("unused") - public static BufferedReader getBuffereReader(Object file) throws FileNotFoundException { - if (file instanceof String) - return new BufferedReader(new FileReader((String) file)); - - byte[] bytes = /** @j2sNative file._bytes || */ null; - if (bytes != null) - return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes))); - return new BufferedReader(new FileReader((File) file)); + private void setShouldBeSaved() + { + if (protocol == null) + return; + AlignFrame af = this.alignFrame; + if (af == null) + return; + AlignViewport avp = af.getViewport(); + if (avp == null) + return; + avp.setSavedUpToDate(!protocol.isDynamic(), + QuitHandler.Message.UNSAVED_ALIGNMENTS); } }