From 94fe396cda7b8f726a57ee62d4e843bb609cfd43 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 4 Sep 2016 17:42:28 +0100 Subject: [PATCH] JAL-1919 preserve filename on restore of project so Chimera recognises mmCIF files from .cif suffix --- src/jalview/gui/Jalview2XML.java | 37 +++++++++++++++++++++++++++---------- 1 file changed, 27 insertions(+), 10 deletions(-) diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 86f8146..a9ff3b8 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -2660,14 +2660,16 @@ public class Jalview2XML * @param pdbId * @return */ - String loadPDBFile(jarInputStreamProvider jprovider, String pdbId) + String loadPDBFile(jarInputStreamProvider jprovider, String pdbId, + String origFile) { if (alreadyLoadedPDB.containsKey(pdbId)) { return alreadyLoadedPDB.get(pdbId).toString(); } - String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb"); + String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb", + origFile); if (tempFile != null) { alreadyLoadedPDB.put(pdbId, tempFile); @@ -2684,14 +2686,26 @@ public class Jalview2XML * @param prefix * a prefix for the temporary file name, must be at least three * characters long + * @param origFile + * null or original file - so new file can be given the same suffix + * as the old one * @return */ protected String copyJarEntry(jarInputStreamProvider jprovider, - String jarEntryName, String prefix) + String jarEntryName, String prefix, String origFile) { BufferedReader in = null; PrintWriter out = null; - + String suffix = ".tmp"; + if (origFile == null) + { + origFile = jarEntryName; + } + int sfpos = origFile.lastIndexOf("."); + if (sfpos > -1 && sfpos < (origFile.length() - 3)) + { + suffix = "." + origFile.substring(sfpos + 1); + } try { JarInputStream jin = jprovider.getJarInputStream(); @@ -2709,7 +2723,7 @@ public class Jalview2XML if (entry != null) { in = new BufferedReader(new InputStreamReader(jin, UTF_8)); - File outFile = File.createTempFile(prefix, ".tmp"); + File outFile = File.createTempFile(prefix, suffix); outFile.deleteOnExit(); out = new PrintWriter(new FileOutputStream(outFile)); String data; @@ -2995,7 +3009,8 @@ public class Jalview2XML { if (!pdbloaded.containsKey(ids[p].getFile())) { - entry.setFile(loadPDBFile(jprovider, ids[p].getId())); + entry.setFile(loadPDBFile(jprovider, ids[p].getId(), + ids[p].getFile())); } else { @@ -3565,7 +3580,7 @@ public class Jalview2XML String rnaTitle = ss.getTitle(); String sessionState = ss.getViewerState(); String tempStateFile = copyJarEntry(jprovider, sessionState, - "varna"); + "varna", null); RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped); appVarna.addModelSession(rna, rnaTitle, tempStateFile); } @@ -3740,7 +3755,8 @@ public class Jalview2XML // Originally : ids[p].getFile() // : TODO: verify external PDB file recovery still works in normal // jalview project load - jpdb.setFile(loadPDBFile(jprovider, ids[p].getId())); + jpdb.setFile(loadPDBFile(jprovider, ids[p].getId(), + ids[p].getFile())); jpdb.setId(ids[p].getId()); int x = structureState.getXpos(); @@ -3751,7 +3767,8 @@ public class Jalview2XML // Probably don't need to do this anymore... // Desktop.desktop.getComponentAt(x, y); // TODO: NOW: check that this recovers the PDB file correctly. - String pdbFile = loadPDBFile(jprovider, ids[p].getId()); + String pdbFile = loadPDBFile(jprovider, ids[p].getId(), + ids[p].getFile()); jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i] .getId() + ""); if (sviewid == null) @@ -3911,7 +3928,7 @@ public class Jalview2XML */ String viewerJarEntryName = getViewerJarEntryName(data.getViewId()); chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName, - "chimera"); + "chimera", null); Set> fileData = data.getFileData() .entrySet(); -- 1.7.10.2