X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=c7ade20da180eea51bb50cc66d5e38c92caf4e8f;hb=c0e43acd458a2e19a5ab3be56a53bc88932657c4;hp=eda3899a13306555a3c15bc0fa13cdb268bd2415;hpb=c945c9641de88cad01b09b3db19e45667dfe751e;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index eda3899..c7ade20 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,12 +20,21 @@ */ 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; import jalview.api.FeaturesSourceI; import jalview.bin.Cache; import jalview.bin.Jalview; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentAnnotation.TFType; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; @@ -33,27 +42,14 @@ 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.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; @@ -79,6 +75,8 @@ public class FileLoader implements Runnable private File selectedFile; + private AlignmentAnnotation.TFType temperatureFactorType = null; + /** * default constructor always raised errors in GUI dialog boxes */ @@ -102,7 +100,8 @@ 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(); } @@ -163,9 +162,44 @@ public class FileLoader implements Runnable public AlignFrame LoadFileWaitTillLoaded(String file, DataSourceType sourceType, FileFormatI format) { + return LoadFileWaitTillLoaded(file, sourceType, format, null); + } + + /** + * Load alignment from (file, protocol) of type format with specified + * temperature factor type and wait till loaded + * + * @param file + * @param sourceType + * @param format + * @param tempfacType + * @return alignFrame constructed from file contents + */ + public AlignFrame LoadFileWaitTillLoaded(String file, + DataSourceType sourceType, FileFormatI format, AlignmentAnnotation.TFType tempfacType) + { this.file = file; this.protocol = sourceType; this.format = format; + this.temperatureFactorType = tempfacType; + return _LoadFileWaitTillLoaded(); + } + + /** + * Load alignment from (file, protocol) of type format and wait till loaded + * + * @param file + * @param sourceType + * @param format + * @return alignFrame constructed from file contents + */ + public AlignFrame LoadFileWaitTillLoaded(File file, + DataSourceType sourceType, FileFormatI format) + { + this.selectedFile = file; + this.file = file.getPath(); + this.protocol = sourceType; + this.format = format; return _LoadFileWaitTillLoaded(); } @@ -196,6 +230,7 @@ public class FileLoader implements Runnable protected AlignFrame _LoadFileWaitTillLoaded() { this.run(); + return alignFrame; } @@ -258,6 +293,7 @@ public class FileLoader implements Runnable ? "Copied From Clipboard" : file; Runtime rt = Runtime.getRuntime(); + try { if (Desktop.instance != null) @@ -272,7 +308,8 @@ 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 @@ -320,7 +357,9 @@ 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 { @@ -348,22 +387,31 @@ public class FileLoader implements Runnable file.lastIndexOf(".")); String tempStructureFileStr = createNamedJvTempFile( urlLeafName, structExt); - UrlDownloadClient.download(file, tempStructureFileStr); - al = fa.readFile(tempStructureFileStr, DataSourceType.FILE, - format); + + // 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); 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, + temperatureFactorType); + + } + else + { + al = fa.readFile(selectedFile, null, protocol, format, + temperatureFactorType); + } source = fa.getAlignFile(); // keep reference for later if - - // necessary. + + // necessary. } } } catch (java.io.IOException ex) @@ -397,12 +445,9 @@ 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 { @@ -443,13 +488,14 @@ public class FileLoader implements Runnable if (!(protocol == DataSourceType.PASTE)) { alignFrame.setFileName(file, format); + alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS } if (proxyColourScheme != null) { alignFrame.getViewport() .applyFeaturesStyle(proxyColourScheme); } - alignFrame.statusBar.setText(MessageManager.formatMessage( + alignFrame.setStatus(MessageManager.formatMessage( "label.successfully_loaded_file", new String[] { title })); @@ -466,8 +512,8 @@ public class FileLoader implements Runnable try { - alignFrame.setMaximum(jalview.bin.Cache - .getDefault("SHOW_FULLSCREEN", false)); + alignFrame.setMaximum( + Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -615,21 +661,4 @@ 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)); - } - }