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[Jmol-commits] SF.net SVN: jmol:[21206]
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From: <ha...@us...> - 2016-08-10 17:34:04
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Revision: 21206
http://sourceforge.net/p/jmol/code/21206
Author: hansonr
Date: 2016-08-10 17:34:01 +0000 (Wed, 10 Aug 2016)
Log Message:
-----------
PyMOL reader upgrade
Modified Paths:
--------------
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
Modified: branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java 2016-08-10 16:23:38 UTC (rev 21205)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java 2016-08-10 17:34:01 UTC (rev 21206)
@@ -105,8 +105,7 @@
}
private int ipt = 0;
- public boolean haveBinaryString;
-
+
@SuppressWarnings("unchecked")
Map<String, Object> getMap(boolean logging)
throws Exception {
@@ -195,8 +194,8 @@
i = binaryDoc.readIntLE();
a = new byte[i];
binaryDoc.readByteArray(a, 0, i);
+ //System.out.println(bytesToString(a));
push(a);
- haveBinaryString = true;
break;
case BINUNICODE:
i = binaryDoc.readIntLE();
@@ -230,8 +229,8 @@
break;
case SETITEM:
o = pop();
- a = (byte[]) pop();
- ((Map<String, Object>) peek()).put(bytesToString(a), o);
+ String s = bytesToString(pop());
+ ((Map<String, Object>) peek()).put(s, o);
break;
case SETITEMS:
mark = getMark();
@@ -244,11 +243,7 @@
map = (Map<String, Object>) o;
for (i = l.size(); --i >= 0;) {
o = l.get(i);
- Object oo = l.get(--i);
- if (AU.isAB(oo))
- map.put(bytesToString((byte[]) oo), o);
- else
- map.put(oo.toString(), o);
+ map.put(bytesToString(l.get(--i)), o);
}
}
break;
@@ -261,7 +256,7 @@
break;
case INT:
/// "0x88000000" for instance
- String s = bytesToString(readStringAsBytes());
+ s = bytesToString(readStringAsBytes());
try {
push(Integer.valueOf(Integer.parseInt(s)));
} catch (Exception e) {
@@ -365,9 +360,9 @@
return map;
}
- private String bytesToString(byte[] a) {
+ private String bytesToString(Object o) {
try {
- return new String(a, "UTF-8");
+ return (AU.isAB(o) ? new String((byte[]) o, "UTF-8") : o.toString());
} catch (UnsupportedEncodingException e) {
return "";
}
Modified: branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2016-08-10 16:23:38 UTC (rev 21205)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2016-08-10 17:34:01 UTC (rev 21206)
@@ -144,7 +144,7 @@
private int bondCount;
- private boolean haveBinaryArrays;
+ private boolean haveBinaryArrays = true;
@Override
protected void setup(String fullPath, Map<String, Object> htParams, Object reader) {
@@ -203,7 +203,6 @@
PickleReader reader = new PickleReader(binaryDoc, vwr);
Map<String, Object> map = reader.getMap(logging && Logger.debuggingHigh);
- haveBinaryArrays = reader.haveBinaryString;
reader = null;
process(map);
}
@@ -274,6 +273,8 @@
// create settings and uniqueSettings lists
Lst<Object> settings = fixSettings(getMapList(map, "settings"));
+ Lst<Object> lst = listAt(settings, PyMOL.dump_binary);
+ haveBinaryArrays = (lst != null && floatAt(lst, 2) == 1);
sceneOrder = getMapList(map, "scene_order");
haveScenes = getFrameScenes(map);
Lst<Object> file = listAt(settings, PyMOL.session_file);
@@ -556,8 +557,10 @@
if (ns > stateCount)
stateCount = ns;
int nAtoms, nBonds;
+ Object o = listAt(pymolObject, 6).get(1);
+ haveBinaryArrays = AU.isAB(o);
if (haveBinaryArrays) {
- nBonds = ((byte[]) listAt(pymolObject, 6).get(1)).length / 20;
+ nBonds = ((byte[]) o).length / 20;
nAtoms = ((byte[]) listAt(pymolObject, 7).get(1)).length / 120;
n += nAtoms;
} else {
@@ -1763,7 +1766,7 @@
}
static float floatAt(Lst<Object> list, int i) {
- return (list == null ? 0 : ((Number) list.get(i)).floatValue());
+ return (list == null || i >= list.size() ? 0 : ((Number) list.get(i)).floatValue());
}
@SuppressWarnings("unchecked")
Modified: branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java 2016-08-10 16:23:38 UTC (rev 21205)
+++ branches/v14_6/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java 2016-08-10 17:34:01 UTC (rev 21206)
@@ -754,7 +754,7 @@
@SuppressWarnings("unchecked")
float globalSetting(int i) {
- Lst<Object> setting = (Lst<Object>) settings.get(i);
+ Lst<Object> setting = PyMOLReader.listAt(settings, i);
if (setting != null && setting.size() == 3)
return ((Number) setting.get(2)).floatValue();
return PyMOL.getDefaultSetting(i, pymolVersion);
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java 2016-08-10 16:23:38 UTC (rev 21205)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PickleReader.java 2016-08-10 17:34:01 UTC (rev 21206)
@@ -105,8 +105,7 @@
}
private int ipt = 0;
- public boolean haveBinaryString;
-
+
@SuppressWarnings("unchecked")
Map<String, Object> getMap(boolean logging)
throws Exception {
@@ -195,8 +194,8 @@
i = binaryDoc.readIntLE();
a = new byte[i];
binaryDoc.readByteArray(a, 0, i);
+ //System.out.println(bytesToString(a));
push(a);
- haveBinaryString = true;
break;
case BINUNICODE:
i = binaryDoc.readIntLE();
@@ -230,8 +229,8 @@
break;
case SETITEM:
o = pop();
- a = (byte[]) pop();
- ((Map<String, Object>) peek()).put(bytesToString(a), o);
+ String s = bytesToString(pop());
+ ((Map<String, Object>) peek()).put(s, o);
break;
case SETITEMS:
mark = getMark();
@@ -244,11 +243,7 @@
map = (Map<String, Object>) o;
for (i = l.size(); --i >= 0;) {
o = l.get(i);
- Object oo = l.get(--i);
- if (AU.isAB(oo))
- map.put(bytesToString((byte[]) oo), o);
- else
- map.put(oo.toString(), o);
+ map.put(bytesToString(l.get(--i)), o);
}
}
break;
@@ -261,7 +256,7 @@
break;
case INT:
/// "0x88000000" for instance
- String s = bytesToString(readStringAsBytes());
+ s = bytesToString(readStringAsBytes());
try {
push(Integer.valueOf(Integer.parseInt(s)));
} catch (Exception e) {
@@ -365,9 +360,9 @@
return map;
}
- private String bytesToString(byte[] a) {
+ private String bytesToString(Object o) {
try {
- return new String(a, "UTF-8");
+ return (AU.isAB(o) ? new String((byte[]) o, "UTF-8") : o.toString());
} catch (UnsupportedEncodingException e) {
return "";
}
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2016-08-10 16:23:38 UTC (rev 21205)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLReader.java 2016-08-10 17:34:01 UTC (rev 21206)
@@ -144,7 +144,7 @@
private int bondCount;
- private boolean haveBinaryArrays;
+ private boolean haveBinaryArrays = true;
@Override
protected void setup(String fullPath, Map<String, Object> htParams, Object reader) {
@@ -203,7 +203,6 @@
PickleReader reader = new PickleReader(binaryDoc, vwr);
Map<String, Object> map = reader.getMap(logging && Logger.debuggingHigh);
- haveBinaryArrays = reader.haveBinaryString;
reader = null;
process(map);
}
@@ -274,6 +273,8 @@
// create settings and uniqueSettings lists
Lst<Object> settings = fixSettings(getMapList(map, "settings"));
+ Lst<Object> lst = listAt(settings, PyMOL.dump_binary);
+ haveBinaryArrays = (lst != null && floatAt(lst, 2) == 1);
sceneOrder = getMapList(map, "scene_order");
haveScenes = getFrameScenes(map);
Lst<Object> file = listAt(settings, PyMOL.session_file);
@@ -556,8 +557,10 @@
if (ns > stateCount)
stateCount = ns;
int nAtoms, nBonds;
+ Object o = listAt(pymolObject, 6).get(1);
+ haveBinaryArrays = AU.isAB(o);
if (haveBinaryArrays) {
- nBonds = ((byte[]) listAt(pymolObject, 6).get(1)).length / 20;
+ nBonds = ((byte[]) o).length / 20;
nAtoms = ((byte[]) listAt(pymolObject, 7).get(1)).length / 120;
n += nAtoms;
} else {
@@ -1763,7 +1766,7 @@
}
static float floatAt(Lst<Object> list, int i) {
- return (list == null ? 0 : ((Number) list.get(i)).floatValue());
+ return (list == null || i >= list.size() ? 0 : ((Number) list.get(i)).floatValue());
}
@SuppressWarnings("unchecked")
Modified: trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java 2016-08-10 16:23:38 UTC (rev 21205)
+++ trunk/Jmol/src/org/jmol/adapter/readers/pymol/PyMOLScene.java 2016-08-10 17:34:01 UTC (rev 21206)
@@ -754,7 +754,7 @@
@SuppressWarnings("unchecked")
float globalSetting(int i) {
- Lst<Object> setting = (Lst<Object>) settings.get(i);
+ Lst<Object> setting = PyMOLReader.listAt(settings, i);
if (setting != null && setting.size() == 3)
return ((Number) setting.get(2)).floatValue();
return PyMOL.getDefaultSetting(i, pymolVersion);
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