X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=7eda11020dc685e9e3ad9563711e622b510a85e8;hb=bba1381449408269047715a41a43115621d1045a;hp=4b2f797ae18183858a5270eab540c91e9a837d1d;hpb=75b38b407cf19737bcc9013a483e1beee32f5523;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 4b2f797..7eda110 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,6 +20,14 @@ */ package jalview.io; +import java.awt.Dimension; +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 +41,15 @@ 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.json.binding.biojson.v1.ColourSchemeMapper; +import jalview.project.Jalview2XML; import jalview.schemes.ColourSchemeI; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; +import jalview.util.Platform; 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; @@ -214,6 +210,7 @@ public class FileLoader implements Runnable protected AlignFrame _LoadFileWaitTillLoaded() { this.run(); + return alignFrame; } @@ -278,9 +275,9 @@ public class FileLoader implements Runnable Runtime rt = Runtime.getRuntime(); try { - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.startLoading(file); + Desktop.getInstance().startLoading(file); } if (format == null) { @@ -302,12 +299,12 @@ public class FileLoader implements Runnable if (format == null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); System.err.println("The input file \"" + file + "\" has null or unidentifiable data content!"); if (!Jalview.isHeadlessMode()) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.couldnt_read_data") + " in " + file + "\n" + AppletFormatAdapter.getSupportedFormats(), @@ -318,7 +315,7 @@ public class FileLoader implements Runnable } // TODO: cache any stream datasources as a temporary file (eg. PDBs // retrieved via URL) - if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) + if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage()) { System.gc(); memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free @@ -338,7 +335,8 @@ 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 { @@ -410,7 +408,7 @@ public class FileLoader implements Runnable // register PDB entries with desktop's structure selection // manager StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + .getStructureSelectionManager(Desktop.getInstance()) .registerPDBEntry(pdbe); } } @@ -473,7 +471,7 @@ public class FileLoader implements Runnable alignFrame.getViewport() .applyFeaturesStyle(proxyColourScheme); } - alignFrame.statusBar.setText(MessageManager.formatMessage( + alignFrame.setStatus(MessageManager.formatMessage( "label.successfully_loaded_file", new String[] { title })); @@ -484,8 +482,12 @@ public class FileLoader implements Runnable // status in Jalview 3 // TODO: define 'virtual desktop' for benefit of headless scripts // that perform queries to find the 'current working alignment' - Desktop.addInternalFrame(alignFrame, title, + + Dimension dim = Platform.getDimIfEmbedded(alignFrame, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + alignFrame.setSize(dim); + Desktop.addInternalFrame(alignFrame, title, dim.width, + dim.height); } try @@ -499,23 +501,23 @@ public class FileLoader implements Runnable } else { - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } 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) + if (raiseGUI && Desktop.getDesktopPane() != null) { javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), errorMessage, MessageManager .getString("label.error_loading_file"), @@ -543,7 +545,7 @@ public class FileLoader implements Runnable @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.formatMessage( "label.problems_opening_file", new String[] { file }), @@ -565,7 +567,7 @@ public class FileLoader implements Runnable @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.formatMessage( "warn.out_of_memory_loading_file", new String[] { file }), @@ -587,7 +589,7 @@ public class FileLoader implements Runnable // memory // after // load - if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) + if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage()) { if (alignFrame != null) { @@ -609,9 +611,9 @@ public class FileLoader implements Runnable } } // remove the visual delay indicator - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } } @@ -639,21 +641,4 @@ 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 - */ - @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)); - } - }