From: <ha...@us...> - 2013-03-31 22:34:14
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Revision: 18034 http://sourceforge.net/p/jmol/code/18034 Author: hansonr Date: 2013-03-31 22:34:11 +0000 (Sun, 31 Mar 2013) Log Message: ----------- for release (2) ___JmolVersion="13.1.14" new feature: JVXL vertex-only data encoding "none" allows hand-coding of JVXL files new feature: isosurface efvet reader data "0" is "indicated colors" -- isosurface "test.efvet" 0 JavaScript: WebGL fix involving Collections.list calling ArrayList.add() JavaScript: disambiguation of Mesh() JavaScript: changing to utf-8 String nonbinary reading of .po files JavaScript: localization working code: cleaning up of Escape and checks for array types code: JavaScript does not need a visible canvas to create images -- could allow for "headless" JS operation bug fix: JVXL 1.0 format reading broken bug fix: MOL2 reader not properly assigning element symbols bug fix: isosurface slab translucent broken when saved in state bug fix: isosurface slab translucent mesh broken when saved in state bug fix: JavaScript minimization fix bug fix: sync socket connections not working bug fix: "navigate percent" broken bug fix: isosurface area/volume broken bug fix: JavaScript WRITE IMAGE with HTML5 does not allow change of width or height bug fix: WRITE PNGJ does not allow sizing of image bug fix: backbone/spine defs do not take into account phosphorylated proteins. Better: "@backbone protein&(_a>=1&_a<6|_a>=64&_a<72)|nucleic&(_a>=6&_a<14|_a>=72)", "@spine protein&_a>=1&_a<4|nucleic&_a>=6&_a<14&_a!=12", bug fix: getProperty fileInfo fixed and documented bug fix: assign atom does not update selections for elements bug fix: FileDropper broken bug fix: LcaoCartoon "-sp3d" not working bug fix: PyMOL PSE files not accessible by Jmol app File...Open or drag/drop bug fix: incorrect calculation of RMSD for COMPARE and SMILES bug fix: ModelKit menu "SHIFT to rotate" should read "ALT to rotate" bug fix: starting applet console takes two clicks bug fix: JavaScript SMILES bug (String.replaceAll() does not work bug fix: JavaScript LOOP command not implemented Modified Paths: -------------- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java =================================================================== --- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java 2013-03-31 21:47:53 UTC (rev 18033) +++ trunk/Jmol/src/org/jmol/jvxl/readers/JvxlReader.java 2013-03-31 22:34:11 UTC (rev 18034) @@ -88,8 +88,12 @@ readVoxelVector(1); readVoxelVector(2); skipComments(true); - for (int i = 0; i < atomCount; ++i) - jvxlFileHeaderBuffer.append(readLine() + "\n"); + for (int i = 0; i < atomCount; ++i) { + jvxlFileHeaderBuffer.append(line + "\n"); + readLine(); + } + if (line.indexOf("#") == 0) + skipComments(true); Logger.info("Reading extra JVXL information line: " + line); nSurfaces = parseIntStr(line); if (!(isJvxl = (nSurfaces < 0))) @@ -110,7 +114,7 @@ colorFractionRange = parseInt(); } cJvxlEdgeNaN = (char)(edgeFractionBase + edgeFractionRange); - + vertexDataOnly = jvxlData.vertexDataOnly = (volumetricVectors[0].length() == 0); } @Override Modified: trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java =================================================================== --- trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2013-03-31 21:47:53 UTC (rev 18033) +++ trunk/Jmol/src/org/jmol/jvxl/readers/JvxlXmlReader.java 2013-03-31 22:34:11 UTC (rev 18034) @@ -734,6 +734,9 @@ } private static String getEncoding(String data) { + // original JVXL does not include "encoding" + if (XmlReader.getXmlAttrib(data, "len").length() > 0) + return ""; String s = XmlReader.getXmlAttrib(data, "encoding"); return (s.length() == 0 ? "none" : s); } @@ -883,9 +886,9 @@ } v += diff; } else { - v = Parser.parseIntNext(tdata, nextp); + v = Parser.parseIntNext(tdata, nextp) - 1; } - vertex[p] = v - 1; + vertex[p] = v; if (++p == 3) { p = 0; if (haveEdgeInfo) { Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-31 21:47:53 UTC (rev 18033) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2013-03-31 22:34:11 UTC (rev 18034) @@ -23,6 +23,7 @@ code: cleaning up of Escape and checks for array types code: JavaScript does not need a visible canvas to create images -- could allow for "headless" JS operation +bug fix: JVXL 1.0 format reading broken bug fix: MOL2 reader not properly assigning element symbols bug fix: isosurface slab translucent broken when saved in state bug fix: isosurface slab translucent mesh broken when saved in state This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |