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[Jmol-commits] SF.net SVN: jmol:[16600] trunk/Jmol/src/org
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From: <ha...@us...> - 2011-12-18 03:54:25
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Revision: 16600
http://jmol.svn.sourceforge.net/jmol/?rev=16600&view=rev
Author: hansonr
Date: 2011-12-18 03:54:17 +0000 (Sun, 18 Dec 2011)
Log Message:
-----------
v.toArray(new XXXXX[v.size()])
Modified Paths:
--------------
trunk/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java
trunk/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java
trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
trunk/Jmol/src/org/jmol/minimize/Minimizer.java
trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
trunk/Jmol/src/org/jmol/script/Token.java
trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
trunk/Jmol/src/org/jmol/util/ArrayUtil.java
trunk/Jmol/src/org/jmol/util/Escape.java
trunk/Jmol/src/org/jmol/util/ZipUtil.java
trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/MdTopReader.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -145,10 +145,7 @@
vdata.add(line.substring(i, i + n).trim());
i += n;
}
- String[] data = new String[vdata.size()];
- for (i = vdata.size(); --i >= 0; )
- data[i] = vdata.get(i);
- return data;
+ return vdata.toArray(new String[vdata.size()]);
}
/*
Modified: trunk/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/adapter/readers/more/P2nReader.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -56,12 +56,9 @@
@Override
protected void finalizeReader() throws Exception {
super.finalizeReader();
- if (useAltNames)
- return;
- String[] names = new String[altNames.size()];
- for (int i = 0; i < names.length; i++)
- names[i] = altNames.get(i);
- atomSetCollection.setAtomSetAuxiliaryInfo("altName", names);
+ if (!useAltNames)
+ atomSetCollection.setAtomSetAuxiliaryInfo("altName", altNames
+ .toArray(new String[altNames.size()]));
}
}
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/Resolver.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -395,10 +395,7 @@
} catch (Exception e) {
//
}
- String[] dirs = new String[v.size()];
- for (int i = 0; i < v.size(); i++)
- dirs[i] = v.get(i);
- return dirs;
+ return v.toArray(new String[v.size()]);
}
private static final String CML_NAMESPACE_URI = "http://www.xml-cml.org/schema";
Modified: trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java
===================================================================
--- trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/adapter/smarter/SmarterJmolAdapter.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -374,7 +374,7 @@
if (ZipUtil.isJmolManifest(thisEntry) || haveManifest
&& exceptFiles == manifest.indexOf("|" + thisEntry + "|") >= 0)
continue;
- byte[] bytes = ZipUtil.getZipEntryAsBytes(zis);
+ byte[] bytes = ZipUtil.getStreamBytes(zis, ze.getSize());
if (ZipUtil.isZipFile(bytes)) {
BufferedInputStream bis = new BufferedInputStream(
new ByteArrayInputStream(bytes));
Modified: trunk/Jmol/src/org/jmol/minimize/Minimizer.java
===================================================================
--- trunk/Jmol/src/org/jmol/minimize/Minimizer.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/minimize/Minimizer.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -605,10 +605,7 @@
+ minAtoms[atomList[ic]].getIdentity());
*/ }
}
-
- angles = new int[vAngles.size()][];
- for (int i = vAngles.size(); --i >= 0; )
- angles[i] = vAngles.get(i);
+ angles = vAngles.toArray(new int[vAngles.size()][]);
Logger.info(angles.length + " angles");
}
@@ -653,11 +650,7 @@
}
}
-
- torsions = new int[vTorsions.size()][];
- for (int i = vTorsions.size(); --i >= 0;)
- torsions[i] = vTorsions.get(i);
-
+ torsions = vTorsions.toArray(new int[vTorsions.size()][]);
Logger.info(torsions.length + " torsions");
}
Modified: trunk/Jmol/src/org/jmol/modelset/ModelCollection.java
===================================================================
--- trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/modelset/ModelCollection.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -1143,11 +1143,7 @@
v.add(q);
i = g.lastAtomIndex;
}
- Quaternion[] qs = new Quaternion[v.size()];
- for (int i = 0; i < qs.length; i++) {
- qs[i] = v.get(i);
- }
- return qs;
+ return v.toArray(new Quaternion[v.size()]);
}
/**
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompilationTokenParser.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -237,9 +237,7 @@
}
}
}
- atokenInfix = new Token[ltokenPostfix.size()];
- for (int i = ltokenPostfix.size(); --i >= 0;)
- atokenInfix[i] = ltokenPostfix.get(i);
+ atokenInfix = ltokenPostfix.toArray(new Token[ltokenPostfix.size()]);
return true;
}
Modified: trunk/Jmol/src/org/jmol/script/ScriptCompiler.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/script/ScriptCompiler.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -426,9 +426,7 @@
}
private void setAaTokenCompiled() {
- aatokenCompiled = new Token[lltoken.size()][];
- for (int i = lltoken.size(); --i >= 0;)
- aatokenCompiled[i] = lltoken.get(i);
+ aatokenCompiled = lltoken.toArray(new Token[lltoken.size()][]);
}
private boolean lookingAtLeadingWhitespace() {
@@ -794,9 +792,7 @@
}
}
- atokenInfix = new Token[size = ltoken.size()];
- for (int i = ltoken.size(); --i >= 0;)
- atokenInfix[i] = ltoken.get(i);
+ atokenInfix = ltoken.toArray(new Token[size = ltoken.size()]);
if (logMessages) {
Logger.debug("token list:");
Modified: trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/script/ScriptEvaluator.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -4390,11 +4390,8 @@
}
if (tok != Token.rightsquare)
error(ERROR_invalidArgument);
- if (points == null) {
- points = new Point3f[vp.size()];
- for (int j = vp.size(); --j >= 0;)
- points[j] = vp.get(j);
- }
+ if (points == null)
+ points = vp.toArray(new Point3f[vp.size()]);
return points;
}
@@ -6604,10 +6601,7 @@
i = iToken;
}
if (v.size() > 0) {
- path = new Point3f[v.size()];
- for (int j = 0; j < v.size(); j++) {
- path[j] = v.get(j);
- }
+ path = v.toArray(new Point3f[v.size()]);
if (!isSyntaxCheck)
viewer.navigate(timeSec, path, theta, 0, Integer.MAX_VALUE);
continue;
@@ -6916,10 +6910,7 @@
}
}
retStddev[0] = 0;
- data1 = new Quaternion[vQ.size()];
- for (int i = vQ.size(); --i >= 0;) {
- data1[i] = vQ.get(i);
- }
+ data1 = vQ.toArray(new Quaternion[vQ.size()]);
q = Quaternion.sphereMean(data1, retStddev, 0.0001f);
showString("RMSD = " + retStddev[0] + " degrees");
} else {
@@ -7095,10 +7086,7 @@
return new String[] {};
}
showString("RMSD " + stddev + " Angstroms");
- b = new BitSet[vReturn.size()];
- for (int j = 0; j < b.length; j++) {
- b[j] = vReturn.get(j);
- }
+ b = vReturn.toArray(new BitSet[vReturn.size()]);
}
if (asOneBitset) {
// sum total of all now, not just first
Modified: trunk/Jmol/src/org/jmol/script/Token.java
===================================================================
--- trunk/Jmol/src/org/jmol/script/Token.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/script/Token.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -1411,9 +1411,7 @@
if (tokAttr(token.tok, attr) && (notattr == nada || !tokAttr(token.tok, notattr)))
v.add(name);
}
- String[] a = new String[v.size()];
- for (int i = 0; i < a.length; i++)
- a[i] = v.get(i);
+ String[] a = v.toArray(new String[v.size()]);
Arrays.sort(a);
return a;
}
Modified: trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java
===================================================================
--- trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/smiles/SmilesMatcher.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -311,7 +311,7 @@
firstMatchOnly, MODE_ARRAY);
}
- @SuppressWarnings({ "unchecked", "cast" })
+ @SuppressWarnings({ "unchecked" })
private Object match(String pattern, JmolNode[] atoms, int atomCount,
BitSet bsSelected, BitSet bsAromatic, boolean isSmarts,
boolean matchAllAtoms, boolean firstMatchOnly,
@@ -326,27 +326,20 @@
search.setSelected(bsSelected);
search.bsRequired = null;//(bsRequired != null && bsRequired.cardinality() > 0 ? bsRequired : null);
search.setRingData(bsAromatic);
- List<Object> vSubstructures;
search.firstMatchOnly = firstMatchOnly;
search.matchAllAtoms = matchAllAtoms;
switch (mode) {
case MODE_BITSET:
search.asVector = false;
- return (BitSet) search.search(false);
+ return search.search(false);
case MODE_ARRAY:
search.asVector = true;
- vSubstructures = (List<Object>) search.search(false);
- BitSet[] bitsets = new BitSet[vSubstructures.size()];
- for (int i = 0; i < bitsets.length; i++)
- bitsets[i] = (BitSet) vSubstructures.get(i);
- return bitsets;
+ List<BitSet> vb = (List<BitSet>) search.search(false);
+ return vb.toArray(new BitSet[vb.size()]);
case MODE_MAP:
search.getMaps = true;
- vSubstructures = (List<Object>) search.search(false);
- int[][] maps = new int[vSubstructures.size()][];
- for (int i = 0; i < maps.length; i++)
- maps[i] = (int[]) vSubstructures.get(i);
- return maps;
+ List<int[]> vl = (List<int[]>) search.search(false);
+ return vl.toArray(new int[vl.size()][]);
}
} catch (Exception e) {
if (InvalidSmilesException.getLastError() == null)
Modified: trunk/Jmol/src/org/jmol/util/ArrayUtil.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ArrayUtil.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/util/ArrayUtil.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -249,9 +249,7 @@
return null;
if (v.size() == 1)
return v.get(0);
- String[] keys = new String[v.size()];
- for (int i = 0; i < keys.length; i++)
- keys[i] = v.get(i);
+ String[] keys = v.toArray(new String[v.size()]);
Arrays.sort(keys);
return keys[n % keys.length];
}
Modified: trunk/Jmol/src/org/jmol/util/Escape.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/Escape.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/util/Escape.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -844,11 +844,7 @@
while (next[0] < data.length() && data.charAt(next[0]) != '"')
next[0]++;
}
- String[] array = new String[v.size()];
- for (int i = 0; i < array.length; i++) {
- array[i] = v.get(i);
- }
- return array;
+ return v.toArray(new String[v.size()]);
}
public static String escapeUrl(String url) {
Modified: trunk/Jmol/src/org/jmol/util/ZipUtil.java
===================================================================
--- trunk/Jmol/src/org/jmol/util/ZipUtil.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/jmol/util/ZipUtil.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -72,15 +72,14 @@
public static boolean isPngZipStream(InputStream is) {
if (isZipFile(is))
return false;
- byte[] abMagic = new byte[55];
try {
is.mark(56);
- is.read(abMagic, 0, 55);
+ byte[] abMagic = getStreamBytes(is, 55);
is.reset();
+ return (abMagic[51] == 'P' && abMagic[52] == 'N' && abMagic[53] == 'G' && abMagic[54] == 'J');
} catch (Exception e) {
- // ignore
}
- return (abMagic[51] == 'P' && abMagic[52] == 'N' && abMagic[53] == 'G' && abMagic[54] == 'J');
+ return false;
}
/**
@@ -94,10 +93,10 @@
public static BufferedInputStream checkPngZipStream(BufferedInputStream bis) {
if (!isPngZipStream(bis))
return bis;
- byte[] data = new byte[74];
+ byte[] data = null;
bis.mark(75);
try {
- bis.read(data, 0, 74);
+ data = getStreamBytes(bis, 74);
bis.reset();
int pt = 0;
for (int i = 64, f = 1; --i > 54; f *= 10)
@@ -105,15 +104,9 @@
int n = 0;
for (int i = 74, f = 1; --i > 64; f *= 10)
n += (data[i] - '0') * f;
- data = new byte[n];
while (pt > 0)
pt -= bis.skip(pt);
- n = data.length;
- pt = 0;
- while (pt < n) {
- pt += bis.read(data, pt, n - pt);
- //System.out.println("ziputil " + pt);
- }
+ data = getStreamBytes(bis, n);
bis.close();
} catch (Throwable e) {
data = new byte[0];
@@ -175,7 +168,7 @@
listing.append(name).append('\n');
String sname = "|" + name.substring(name.lastIndexOf("/") + 1) + "|";
boolean asBinaryString = (binaryFileList.indexOf(sname) >= 0);
- byte[] bytes = getZipEntryAsBytes(zis);
+ byte[] bytes = getStreamBytes(zis, ze.getSize());
String str;
if (asBinaryString) {
str = getBinaryStringForBytes(bytes);
@@ -243,7 +236,7 @@
while ((ze = zis.getNextEntry()) != null) {
if (!fileName.equals(ze.getName()))
continue;
- byte[] bytes = getZipEntryAsBytes(zis);
+ byte[] bytes = getStreamBytes(zis, ze.getSize());
//System.out.println("ZipUtil::ZipEntry.name = " + ze.getName() + " " + bytes.length);
if (isZipFile(bytes))
return getZipFileContents(new BufferedInputStream(
@@ -276,7 +269,7 @@
while ((ze = zis.getNextEntry()) != null) {
if (!fileName.equals(ze.getName()))
continue;
- byte[] bytes = getZipEntryAsBytes(zis);
+ byte[] bytes = getStreamBytes(zis, ze.getSize());
if (isZipFile(bytes) && list != null && ++listPtr < list.length)
return getZipFileContentsAsBytes(new BufferedInputStream(
new ByteArrayInputStream(bytes)), list, listPtr);
@@ -332,13 +325,10 @@
zis.close();
if (addManifest)
v.add(0, manifest == null ? "" : manifest + "\n############\n");
- int len = v.size();
- String[] dirList = new String[len];
- for (int i = 0; i < len; i++)
- dirList[i] = v.get(i);
- return dirList;
+ return v.toArray(new String[v.size()]);
}
-
+
+
private static String getZipEntryAsString(InputStream is) throws IOException {
StringBuffer sb = new StringBuffer();
byte[] buf = new byte[1024];
@@ -348,20 +338,24 @@
return sb.toString();
}
- public static byte[] getZipEntryAsBytes(ZipInputStream zis) throws IOException {
+ public static byte[] getStreamBytes(InputStream is, long n) throws IOException {
- //What is the efficient way to read an input stream into a byte array?
+ //Note: You cannot use InputStream.available() to reliably read
+ // zip data from the web.
- byte[] buf = new byte[1024];
- byte[] bytes = new byte[4096];
+ byte[] buf = new byte[n >= 0 && n < 1024 ? (int) n : 1024];
+ byte[] bytes = new byte[n < 0 ? 4096 : (int) n];
int len = 0;
int totalLen = 0;
- while (zis.available() == 1 && (len = zis.read(buf)) > 0) {
+ while ((n < 0 || totalLen < n)
+ && (len = is.read(buf)) > 0) {
totalLen += len;
- if (totalLen >= bytes.length)
+ if (totalLen > bytes.length)
bytes = ArrayUtil.ensureLength(bytes, totalLen * 2);
System.arraycopy(buf, 0, bytes, totalLen - len, len);
}
+ if (totalLen == bytes.length)
+ return bytes;
buf = new byte[totalLen];
System.arraycopy(bytes, 0, buf, 0, totalLen);
return buf;
Modified: trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java
===================================================================
--- trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java 2011-12-17 20:25:51 UTC (rev 16599)
+++ trunk/Jmol/src/org/openscience/jmol/app/jmolpanel/JmolPanel.java 2011-12-18 03:54:17 UTC (rev 16600)
@@ -798,23 +798,14 @@
* for trying to get an array of strings out of the
* resource file.
* @param input String to chop
- * @return Strings chopped on whitespace boundries
+ * @return Strings chopped on whitespace boundaries
*/
protected String[] tokenize(String input) {
-
List<String> v = new ArrayList<String>();
StringTokenizer t = new StringTokenizer(input);
- String cmd[];
-
- while (t.hasMoreTokens()) {
+ while (t.hasMoreTokens())
v.add(t.nextToken());
- }
- cmd = new String[v.size()];
- for (int i = 0; i < cmd.length; i++) {
- cmd[i] = v.get(i);
- }
-
- return cmd;
+ return v.toArray(new String[v.size()]);
}
/**
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