X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;fp=src%2Fjalview%2Fio%2FFileLoader.java;h=d744fae723bdb5a568c8c189afeac3159c797a45;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=c7c1d716bbe822bb2eea453df751f20c34dc9741;hpb=61ff8fb4efa315c35149c9d11850d99e3d00c441;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index c7c1d71..d744fae 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,6 +20,7 @@ */ package jalview.io; +import java.awt.Dimension; import java.io.File; import java.io.IOException; import java.util.StringTokenizer; @@ -46,10 +47,14 @@ 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.util.ArrayList; +import java.util.List; public class FileLoader implements Runnable { + private static final String TAB = "\t"; String file; DataSourceType protocol; @@ -212,56 +217,78 @@ public class FileLoader implements Runnable return alignFrame; } - public void updateRecentlyOpened() + public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport, + String file, DataSourceType sourceType, FileFormatI format) { Vector recent = new Vector<>(); if (protocol == DataSourceType.PASTE) + this.viewport = viewport; + this.file = file; + this.protocol = sourceType; + this.format = format; + _LoadFileWaitTillLoaded(); + } + + + /** + * Updates (or creates) the tab-separated list of recently opened files held + * under the given property name by inserting the filePath at the front of the + * list. Duplicates are removed, and the list is limited to 11 entries. The + * method returns the updated value of the property. + * + * @param filePath + * @param sourceType + */ + public static String updateRecentlyOpened(String filePath, + DataSourceType sourceType) + { + if (sourceType != DataSourceType.FILE + && sourceType != DataSourceType.URL) { - // do nothing if the file was pasted in as text... there is no filename to - // refer to it as. - return; + return null; } - if (file != null - && file.indexOf(System.getProperty("java.io.tmpdir")) > -1) + String propertyName = sourceType == DataSourceType.FILE ? "RECENT_FILE" + : "RECENT_URL"; + String historyItems = Cache.getProperty(propertyName); + if (filePath != null + && filePath.indexOf(System.getProperty("java.io.tmpdir")) > -1) { // ignore files loaded from the system's temporary directory - return; + return null; } - String type = protocol == DataSourceType.FILE ? "RECENT_FILE" - : "RECENT_URL"; - String historyItems = Cache.getProperty(type); - - StringTokenizer st; + List recent = new ArrayList<>(); if (historyItems != null) { - st = new StringTokenizer(historyItems, "\t"); + StringTokenizer st = new StringTokenizer(historyItems, TAB); while (st.hasMoreTokens()) { - recent.addElement(st.nextToken().trim()); + String trimmed = st.nextToken().trim(); + recent.add(trimmed); } } - if (recent.contains(file)) + /* + * if file was already in the list, it moves to the top + */ + if (recent.contains(filePath)) { - recent.remove(file); + recent.remove(filePath); } - StringBuffer newHistory = new StringBuffer(file); + StringBuilder newHistory = new StringBuilder(filePath); for (int i = 0; i < recent.size() && i < 10; i++) { - newHistory.append("\t"); - newHistory.append(recent.elementAt(i)); + newHistory.append(TAB); + newHistory.append(recent.get(i)); } - Cache.setProperty(type, newHistory.toString()); + String newProperty = newHistory.toString(); + Cache.setProperty(propertyName, newProperty); - if (protocol == DataSourceType.FILE) - { - Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName()); - } + return newProperty; } @Override @@ -273,9 +300,9 @@ 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) { @@ -297,12 +324,12 @@ 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(), @@ -313,7 +340,7 @@ 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 @@ -406,7 +433,7 @@ public class FileLoader implements Runnable // register PDB entries with desktop's structure selection // manager StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + .getStructureSelectionManager(Desktop.getInstance()) .registerPDBEntry(pdbe); } } @@ -416,9 +443,29 @@ public class FileLoader implements Runnable .getFeatureColourScheme(); if (viewport != null) { + // TODO: test if this needs to be done after addAlignment ? (like in 2.11.2) + if (proxyColourScheme != null) + { + viewport.applyFeaturesStyle(proxyColourScheme); + } // append to existing alignment viewport.addAlignment(al, title); - viewport.applyFeaturesStyle(proxyColourScheme); + if (source instanceof HMMFile) + { + AlignmentI alignment = viewport.getAlignment(); + SequenceI seq = alignment + .getSequenceAt(alignment.getHeight() - 1); + if (seq.hasHMMProfile()) + { + /* + * fudge: move HMM consensus sequence from last to first + */ + alignment.deleteSequence(alignment.getAbsoluteHeight() - 1); + alignment.insertSequenceAt(0, seq); + } + viewport.getAlignPanel().adjustAnnotationHeight(); + viewport.updateSequenceIdColours(); + } } else { @@ -458,8 +505,7 @@ public class FileLoader implements Runnable // add metadata and update ui if (!(protocol == DataSourceType.PASTE)) { - alignFrame.setFileName(file, format); - alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS + alignFrame.setFile(file, selectedFile, protocol, format); } if (proxyColourScheme != null) { @@ -477,8 +523,12 @@ 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 @@ -492,23 +542,23 @@ 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"), @@ -523,7 +573,12 @@ public class FileLoader implements Runnable } } - updateRecentlyOpened(); + updateRecentlyOpened(file, protocol); + + if (protocol == DataSourceType.FILE && format != null) + { + Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName()); + } } catch (Exception er) { @@ -536,7 +591,7 @@ 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 }), @@ -558,7 +613,7 @@ 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 }), @@ -580,7 +635,7 @@ 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) { @@ -602,9 +657,9 @@ public class FileLoader implements Runnable } } // remove the visual delay indicator - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } }