-import jalview.gui.*;\r
-import jalview.io.*;\r
-\r
-def class JvLoadTest {\r
- FileLoader fl = null;\r
- def String safename = null;\r
- JvLoadTest(String sname) { \r
- if (!new File(sname).exists() || new File(sname).canWrite())\r
- {\r
- safename = sname;\r
- } else {\r
- System.err.println("Warning : "+sname+" isn't being used to store temporary files.");\r
- } \r
- }\r
- def public boolean doTest (file) {\r
- fl = new FileLoader(false);\r
- System.gc();\r
- AlignFrame af = fl.LoadFileWaitTillLoaded(file\r
- ,FormatAdapter.FILE);\r
- return doTest(af);\r
- }\r
- def public boolean doSequentialReadTest (file) {\r
- return doSequentialReadTest(file, 0);\r
- }\r
- // Return true if there is more data to read.\r
- def public boolean peekFp(FileParse fp) {\r
- try { fp.mark(); } catch (Exception ex) { System.err.println("FAILED mark."+ex); return false; };\r
- try {\r
- def String nl;\r
- for (i in 1..3) { \r
- nl = fp.nextLine();\r
- if (nl==null) { return false; }\r
- System.out.println(nl +"\\n");\r
- }\r
- } catch (Exception e) { // end of file.\r
- return false; };\r
- try { fp.reset(); } catch (Exception ex) { System.err.println("FAILED rewind."+ex); return false; };\r
- return true;\r
- }\r
- /*\r
- Halt after loading the mx'th entry in the filestream\r
- */\r
- def public boolean doSequentialReadTest (file, int mx) {\r
- // first properly open the file\r
- // if (!doTest(file)) { return };\r
- def FileParse fp = null;\r
- try {\r
- fp = new FileParse(file, AppletFormatAdapter.FILE);\r
- } catch (Exception e) { System.err.println("Couldn't open "+file+"\\n"); e.printStackTrace(); return false;};\r
- Desktop.instance.closeAll_actionPerformed(null)\r
- System.gc();\r
- while (fp!=null && fp.isValid() && (mx==0 || mx!=fp.index)) {\r
- if (!peekFp(fp)) return false;\r
- fl = new FileLoader(false);\r
- AlignFrame af = fl.LoadFileWaitTillLoaded(fp, null);\r
- System.out.println("FileParse index: "+fp.index); \r
- if (af!=null && (mx==0 || mx!=fp.index))\r
- { def boolean res = doTest(af);\r
- if (!res)\r
- {\r
- // return false;\r
- }\r
- } else {\r
- // return false;\r
- }\r
- }\r
- return true;\r
- }\r
- def public void waitTillSettled(AlignFrame af)\r
- {\r
- if (af==null) { return; }\r
- Thread.sleep(10);\r
- while (af.getViewport().updatingConsensus || af.getViewport().updatingConservation) {\r
- Thread.sleep(150); // wait until things settle down\r
- }\r
- }\r
- def public boolean doTest(AlignFrame af) {\r
- Object pr = af.getViewport().getAlignment().getProperty("AC");\r
- if (pr!=null) { System.out.println("Accession = "+(String) pr); }\r
- af.selectAllSequenceMenuItem_actionPerformed(null)\r
- def boolean done = false;\r
- // Just try to save - don\'t mess around with clipboard\r
- /*while (!done) {\r
- try {\r
- af.copy_actionPerformed(null)\r
- done = true;\r
- } catch (Exception e) {\r
- Thread.sleep(100); // wait until clipboard might be available again\r
- }\r
- }*/\r
- if (af==null) { return false; }\r
- waitTillSettled(af);\r
- // Try and save as a jalview project and reload\r
- try {\r
- // af.saveAlignment(safename, "Jalview")\r
- new Jalview2XML().SaveState(new java.io.File(safename));\r
- Thread.sleep(100);\r
- } catch (Exception ex) { \r
- System.out.println("Couldn\'t save.");\r
- ex.printStackTrace(System.err);\r
- return false;\r
- }\r
- waitTillSettled(af);\r
- try {\r
- Desktop.instance.closeAll_actionPerformed(null);\r
- } catch (Exception ex) {}\r
- System.gc();\r
- try {\r
- af = new FileLoader(false).LoadFileWaitTillLoaded(safename, FormatAdapter.FILE); \r
- } \r
- catch (Exception ex) {\r
- System.out.println("Couldn't reload saved file.");\r
- System.gc();\r
- return false;\r
- }\r
- waitTillSettled(af);\r
-\r
- Desktop.instance.closeAll_actionPerformed(null);\r
-\r
- // af.paste(true)\r
- // af.newView_actionPerformed(null)\r
- // af.newView_actionPerformed(null)\r
-\r
- return true;\r
- }\r
- def public boolean TestForAll(String dir) {\r
- println "For directory or file : "+dir;\r
- File fd = new File(dir);\r
- if (!fd.isDirectory()) { return doSequentialReadTest(dir); }\r
- fd.eachFile() { file -> TestForAll(file.getAbsolutePath()) };\r
- }\r
-}\r
-def JvLoadTest newJvLoadTest(String tempFile) {\r
- jalview.gui.Desktop.instance.closeAll_actionPerformed(null);\r
- System.gc();\r
- jalview.gui.Desktop.instance.desktop.showMemoryUsage(true);\r
- return new JvLoadTest(tempFile)\r
-}
\ No newline at end of file
+/*
+ * 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.*;
+
+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)
+}
git://source.jalview.org / jalview.git / blobdiff