+++ /dev/null
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-import jalview.gui.*;
-import jalview.io.*;
-
-def class JvLoadTest {
- FileLoader fl = null;
- def String safename = null;
- JvLoadTest(String sname) {
- if (!new File(sname).exists() || new File(sname).canWrite())
- {
- safename = sname;
- } else {
- System.err.println("Warning : "+sname+" isn't being used to store temporary files.");
- }
- }
- def public boolean doTest (file) {
- fl = new FileLoader(false);
- System.gc();
- AlignFrame af = fl.LoadFileWaitTillLoaded(file
- ,FormatAdapter.FILE);
- return doTest(af);
- }
- def public boolean doSequentialReadTest (file) {
- return doSequentialReadTest(file, 0);
- }
- // Return true if there is more data to read.
- def public boolean peekFp(FileParse fp) {
- try { fp.mark(); } catch (Exception ex) { System.err.println("FAILED mark."+ex); return false; };
- try {
- def String nl;
- for (i in 1..3) {
- nl = fp.nextLine();
- if (nl==null) { return false; }
- System.out.println(nl +"\\n");
- }
- } catch (Exception e) { // end of file.
- return false; };
- try { fp.reset(); } catch (Exception ex) { System.err.println("FAILED rewind."+ex); return false; };
- return true;
- }
- /*
- Halt after loading the mx'th entry in the filestream
- */
- def public boolean doSequentialReadTest (file, int mx) {
- // first properly open the file
- // if (!doTest(file)) { return };
- def FileParse fp = null;
- try {
- fp = new FileParse(file, AppletFormatAdapter.FILE);
- } catch (Exception e) { System.err.println("Couldn't open "+file+"\\n"); e.printStackTrace(); return false;};
- Desktop.instance.closeAll_actionPerformed(null)
- System.gc();
- while (fp!=null && fp.isValid() && (mx==0 || mx!=fp.index)) {
- if (!peekFp(fp)) return false;
- fl = new FileLoader(false);
- AlignFrame af = fl.LoadFileWaitTillLoaded(fp, null);
- System.out.println("FileParse index: "+fp.index);
- if (af!=null && (mx==0 || mx!=fp.index))
- { def boolean res = doTest(af);
- if (!res)
- {
- // return false;
- }
- } else {
- // return false;
- }
- }
- return true;
- }
- def public void waitTillSettled(AlignFrame af)
- {
- if (af==null) { return; }
- Thread.sleep(10);
- while (af.getViewport().updatingConsensus || af.getViewport().updatingConservation) {
- Thread.sleep(150); // wait until things settle down
- }
- }
- def public boolean doTest(AlignFrame af) {
- Object pr = af.getViewport().getAlignment().getProperty("AC");
- if (pr!=null) { System.out.println("Accession = "+(String) pr); }
- af.selectAllSequenceMenuItem_actionPerformed(null)
- def boolean done = false;
- // Just try to save - don\'t mess around with clipboard
- /*while (!done) {
- try {
- af.copy_actionPerformed(null)
- done = true;
- } catch (Exception e) {
- Thread.sleep(100); // wait until clipboard might be available again
- }
- }*/
- if (af==null) { return false; }
- waitTillSettled(af);
- // Try and save as a jalview project and reload
- try {
- // af.saveAlignment(safename, "Jalview")
- new Jalview2XML().SaveState(new java.io.File(safename));
- Thread.sleep(100);
- } catch (Exception ex) {
- System.out.println("Couldn\'t save.");
- ex.printStackTrace(System.err);
- return false;
- }
- waitTillSettled(af);
- try {
- Desktop.instance.closeAll_actionPerformed(null);
- } catch (Exception ex) {}
- System.gc();
- try {
- af = new FileLoader(false).LoadFileWaitTillLoaded(safename, FormatAdapter.FILE);
- }
- catch (Exception ex) {
- System.out.println("Couldn't reload saved file.");
- System.gc();
- return false;
- }
- waitTillSettled(af);
-
- Desktop.instance.closeAll_actionPerformed(null);
-
- // af.paste(true)
- // af.newView_actionPerformed(null)
- // af.newView_actionPerformed(null)
-
- return true;
- }
- def public boolean TestForAll(String dir) {
- println "For directory or file : "+dir;
- File fd = new File(dir);
- if (!fd.isDirectory()) { return doSequentialReadTest(dir); }
- fd.eachFile() { file -> TestForAll(file.getAbsolutePath()) };
- }
-}
-def JvLoadTest newJvLoadTest(String tempFile) {
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
- System.gc();
- jalview.gui.Desktop.instance.desktop.showMemoryUsage(true);
- return new JvLoadTest(tempFile)
-}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff