X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=fa104a6d3e1c065632fae40fafaa017303379dae;hb=d4ae9b928a7cf73f265adc42f3c83e4ec1f7c3d7;hp=02b405ed0816b268c9f34772234458a5cbccd3a8;hpb=fceb361f2da8878902f9726ab694947f5317e153;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 02b405e..fa104a6 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -38,6 +38,7 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; import jalview.datamodel.GraphLine; import jalview.datamodel.PDBEntry; import jalview.datamodel.Point; @@ -152,6 +153,7 @@ import java.awt.Color; import java.awt.Font; import java.awt.Rectangle; import java.io.BufferedReader; +import java.io.ByteArrayInputStream; import java.io.DataInputStream; import java.io.DataOutputStream; import java.io.File; @@ -208,6 +210,27 @@ import javax.xml.stream.XMLStreamReader; */ public class Jalview2XML { + + // BH 2018 we add the .jvp binary extension to J2S so that + // it will declare that binary when we do the file save from the browser + + private static void addJ2SBinaryType(String ext) + { + ext = "." + ext + "?"; + + /** + * @j2sNative + * + * J2S._binaryTypes.push(ext); + * + */ + } + + static + { + addJ2SBinaryType(".jvp?"); + } + private static final String VIEWER_PREFIX = "viewer_"; private static final String RNA_PREFIX = "rna_"; @@ -745,9 +768,10 @@ public class Jalview2XML try { // create backupfiles object and get new temp filename destination - BackupFiles backupfiles = new BackupFiles(jarFile); - FileOutputStream fos = new FileOutputStream( - backupfiles.getTempFilePath()); + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null; + FileOutputStream fos = new FileOutputStream(doBackup ? + backupfiles.getTempFilePath() : jarFile); JarOutputStream jout = new JarOutputStream(fos); List frames = new ArrayList<>(); @@ -772,8 +796,11 @@ public class Jalview2XML jout.close(); boolean success = true; - backupfiles.setWriteSuccess(success); - success = backupfiles.rollBackupsAndRenameTempFile(); + if (doBackup) + { + backupfiles.setWriteSuccess(success); + success = backupfiles.rollBackupsAndRenameTempFile(); + } return success; } catch (Exception ex) @@ -1659,6 +1686,7 @@ public class Jalview2XML // using save and then load try { + fileName = fileName.replace('\\', '/'); System.out.println("Writing jar entry " + fileName); JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); @@ -2029,6 +2057,7 @@ public class Jalview2XML { if (jout != null) { + jarEntryName = jarEntryName.replace('\\','/'); System.out.println("Writing jar entry " + jarEntryName); jout.putNextEntry(new JarEntry(jarEntryName)); DataOutputStream dout = new DataOutputStream(jout); @@ -2489,7 +2518,7 @@ public class Jalview2XML vamsasSeq.setName(jds.getName()); vamsasSeq.setSequence(jds.getSequenceAsString()); vamsasSeq.setDescription(jds.getDescription()); - jalview.datamodel.DBRefEntry[] dbrefs = null; + List dbrefs = null; if (jds.getDatasetSequence() != null) { vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); @@ -2507,15 +2536,16 @@ public class Jalview2XML } if (dbrefs != null) { - for (int d = 0; d < dbrefs.length; d++) + for (int d = 0, nd = dbrefs.size(); d < nd; d++) { DBRef dbref = new DBRef(); - dbref.setSource(dbrefs[d].getSource()); - dbref.setVersion(dbrefs[d].getVersion()); - dbref.setAccessionId(dbrefs[d].getAccessionId()); - if (dbrefs[d].hasMap()) + DBRefEntry ref = dbrefs.get(d); + dbref.setSource(ref.getSource()); + dbref.setVersion(ref.getVersion()); + dbref.setAccessionId(ref.getAccessionId()); + if (ref.hasMap()) { - Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq, + Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds, recurse); dbref.setMapping(mp); } @@ -2711,7 +2741,7 @@ public class Jalview2XML * @param file * - HTTP URL or filename */ - public AlignFrame loadJalviewAlign(final String file) + public AlignFrame loadJalviewAlign(final Object file) { jalview.gui.AlignFrame af = null; @@ -2755,44 +2785,52 @@ public class Jalview2XML return af; } - private jarInputStreamProvider createjarInputStreamProvider( - final String file) throws MalformedURLException - { - URL url = null; - errorMessage = null; - uniqueSetSuffix = null; - seqRefIds = null; - viewportsAdded.clear(); - frefedSequence = null; - - if (file.startsWith("http://")) - { - url = new URL(file); - } - final URL _url = url; - return new jarInputStreamProvider() - { - - @Override - public JarInputStream getJarInputStream() throws IOException - { - if (_url != null) - { - return new JarInputStream(_url.openStream()); - } - else - { - return new JarInputStream(new FileInputStream(file)); - } - } - - @Override - public String getFilename() - { - return file; - } - }; - } + @SuppressWarnings("unused") + private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException { + + // BH 2018 allow for bytes already attached to File object + try { + String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString()); + byte[] bytes = /** @j2sNative ofile._bytes || */ + null; + URL url = null; + errorMessage = null; + uniqueSetSuffix = null; + seqRefIds = null; + viewportsAdded.clear(); + frefedSequence = null; + + if (file.startsWith("http://")) { + url = new URL(file); + } + final URL _url = url; + return new jarInputStreamProvider() { + + @Override + public JarInputStream getJarInputStream() throws IOException { + if (bytes != null) { +// System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length); + return new JarInputStream(new ByteArrayInputStream(bytes)); + } + if (_url != null) { +// System.out.println("Jalview2XML: opening url jarInputStream for " + _url); + return new JarInputStream(_url.openStream()); + } else { +// System.out.println("Jalview2XML: opening file jarInputStream for " + file); + return new JarInputStream(new FileInputStream(file)); + } + } + + @Override + public String getFilename() { + return file; + } + }; + } catch (IOException e) { + e.printStackTrace(); + return null; + } + } /** * Recover jalview session from a jalview project archive. Caller may @@ -2834,9 +2872,6 @@ public class Jalview2XML if (jarentry != null && jarentry.getName().endsWith(".xml")) { - InputStreamReader in = new InputStreamReader(jin, UTF_8); - // JalviewModel object = new JalviewModel(); - JAXBContext jc = JAXBContext .newInstance("jalview.xml.binding.jalview"); XMLStreamReader streamReader = XMLInputFactory.newInstance() @@ -2846,11 +2881,6 @@ public class Jalview2XML .unmarshal(streamReader, JalviewModel.class); JalviewModel object = jbe.getValue(); - /* - Unmarshaller unmar = new Unmarshaller(object); - unmar.setValidation(false); - object = (JalviewModel) unmar.unmarshal(in); - */ if (true) // !skipViewport(object)) { _af = loadFromObject(object, file, true, jprovider); @@ -4839,7 +4869,18 @@ public class Jalview2XML { AlignFrame af = null; af = new AlignFrame(al, safeInt(view.getWidth()), - safeInt(view.getHeight()), uniqueSeqSetId, viewId); + safeInt(view.getHeight()), uniqueSeqSetId, viewId) +// { +// +// @Override +// protected void processKeyEvent(java.awt.event.KeyEvent e) { +// System.out.println("Jalview2XML AF " + e); +// super.processKeyEvent(e); +// +// } +// +// } + ; af.setFileName(file, FileFormat.Jalview);