Revision: 20892
http://sourceforge.net/p/jmol/code/20892
Author: hansonr
Date: 2015-12-17 18:58:19 +0000 (Thu, 17 Dec 2015)
Log Message:
-----------
Jmol.___JmolVersion="14.5.1_2015.12.16"
bug fix: array handling for labels very inefficient
Modified Paths:
--------------
branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java
branches/v14_4/Jmol/src/org/jmol/shape/Balls.java
branches/v14_4/Jmol/src/org/jmol/shape/Labels.java
branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
Modified: branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2015-12-15 23:16:31 UTC (rev 20891)
+++ branches/v14_4/Jmol/src/org/jmol/adapter/readers/pymol/JmolObject.java
2015-12-17 18:58:19 UTC (rev 20892)
@@ -187,7 +187,7 @@
return;
case JC.SHAPE_LABELS:
sm.loadShape(id);
- sm.setShapePropertyBs(id, "textLabels", info, bsAtoms);
+ sm.setShapePropertyBs(id, "pymolLabels", info, bsAtoms);
return;
case T.bonds:
break;
Modified: branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java 2015-12-15
23:16:31 UTC (rev 20891)
+++ branches/v14_4/Jmol/src/org/jmol/shape/AtomShape.java 2015-12-17
18:58:19 UTC (rev 20892)
@@ -105,11 +105,11 @@
if (atoms == null) // vector values are ignored if there are none for a
model
return;
isActive = true;
- if (bsSizeSet == null)
- bsSizeSet = new BS();
boolean isVisible = (rd != null && rd.value != 0);
boolean isAll = (bsSelected == null);
int i0 = (isAll ? ac - 1 : bsSelected.nextSetBit(0));
+ if (bsSizeSet == null)
+ bsSizeSet = BS.newN(ac);
if (mads == null && i0 >= 0)
mads = new short[ac];
for (int i = i0; i >= 0; i = (isAll ? i - 1 : bsSelected.nextSetBit(i +
1)))
@@ -128,9 +128,8 @@
isActive = true;
short colix = C.getColixO(value);
byte pid = PAL.pidOf(value);
- if (bsColixSet == null)
- bsColixSet = new BS();
- for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1))
+ int n = checkColixLength(colix, bs.length());
+ for (int i = bs.nextSetBit(0); i >= 0 && i < n; i = bs.nextSetBit(i + 1))
setColixAndPalette(colix, pid, i);
return;
}
@@ -142,14 +141,13 @@
float[] sizes = (float[]) data[2];
RadiusData rd = new RadiusData(null, 0, RadiusData.EnumType.FACTOR,
VDW.AUTO);
- if (bsColixSet == null)
- bsColixSet = new BS();
if (bsSizeSet == null)
bsSizeSet = new BS();
int i0 = bs.nextSetBit(0);
if (mads == null && i0 >= 0)
mads = new short[ac];
- for (int i = i0, pt = 0; i >= 0; i = bs.nextSetBit(i + 1), pt++) {
+ int n = checkColixLength(colixes == null ? 0 : C.BLACK, bs.length());
+ for (int i = i0, pt = 0; i >= 0 && i < n; i = bs.nextSetBit(i + 1),
pt++) {
short colix = (colixes == null ? 0 : colixes[pt]);
if (colix == 0)
colix = C.INHERIT_ALL;
@@ -200,15 +198,20 @@
setPropS(propertyName, value, bs);
}
+ protected int checkColixLength(short colix, int n) {
+ n = Math.min(ac, n);
+ if (colix == C.INHERIT_ALL)
+ return (colixes == null ? 0 : colixes.length);
+ if (colixes == null || n > colixes.length) {
+ colixes = AU.ensureLengthShort(colixes, n);
+ paletteIDs = AU.ensureLengthByte(paletteIDs, n);
+ if (bsColixSet == null)
+ bsColixSet = BS.newN(ac);
+ }
+ return n;
+ }
+
protected void setColixAndPalette(short colix, byte paletteID, int
atomIndex) {
- if (colixes == null || atomIndex >= colixes.length) {
- if (colix == C.INHERIT_ALL)
- return;
- colixes = AU.ensureLengthShort(colixes, atomIndex + 1);
- paletteIDs = AU.ensureLengthByte(paletteIDs, atomIndex + 1);
- }
- if (bsColixSet == null)
- bsColixSet = BS.newN(ac);
colixes[atomIndex] = colix = getColixI(colix, paletteID, atomIndex);
bsColixSet.setBitTo(atomIndex, colix != C.INHERIT_ALL);
paletteIDs[atomIndex] = paletteID;
Modified: branches/v14_4/Jmol/src/org/jmol/shape/Balls.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shape/Balls.java 2015-12-15 23:16:31 UTC
(rev 20891)
+++ branches/v14_4/Jmol/src/org/jmol/shape/Balls.java 2015-12-17 18:58:19 UTC
(rev 20892)
@@ -68,7 +68,7 @@
if (colix == C.INHERIT_ALL)
colix = C.USE_PALETTE;
if (bsColixSet == null)
- bsColixSet = new BS();
+ bsColixSet = BS.newN(ac);
byte pid = PAL.pidOf(value);
for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) {
Atom atom = atoms[i];
Modified: branches/v14_4/Jmol/src/org/jmol/shape/Labels.java
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/shape/Labels.java 2015-12-15 23:16:31 UTC
(rev 20891)
+++ branches/v14_4/Jmol/src/org/jmol/shape/Labels.java 2015-12-17 18:58:19 UTC
(rev 20892)
@@ -84,6 +84,8 @@
defaultColix = 0; //"none" -- inherit from atom
defaultBgcolix = 0; //"none" -- off
defaultOffset = JC.LABEL_DEFAULT_OFFSET;
+ defaultAlignment = JC.TEXT_ALIGN_LEFT;
+ defaultPointer = JC.LABEL_POINTER_NONE;
defaultZPos = 0;
translucentAllowed = false;
}
@@ -101,10 +103,12 @@
if ("color" == propertyName) {
byte pid = PAL.pidOf(value);
short colix = C.getColixO(value);
- if (!setDefaults)
- for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
+ if (!setDefaults) {
+ int n = checkColixLength(colix, bsSelected.length());
+ for (int i = bsSelected.nextSetBit(0); i >= 0 && i < n; i = bsSelected
.nextSetBit(i + 1))
setLabelColix(i, colix, pid);
+ }
if (setDefaults || !defaultsOnlyForNone) {
defaultColix = colix;
defaultPaletteID = pid;
@@ -117,10 +121,9 @@
return;
float val = ((Float) value).floatValue();
float scalePixelsPerMicron = (val == 0 ? 0 : 10000f / val);
- for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
+ int n = Math.min(ac, strings.length);
+ for (int i = bsSelected.nextSetBit(0); i >= 0 && i < n; i = bsSelected
.nextSetBit(i + 1)) {
- if (strings.length <= i)
- continue;
Text text = getLabel(i);
if (text == null) {
text = Text.newLabel(vwr, null, strings[i], C.INHERIT_ALL, (short) 0,
@@ -136,15 +139,16 @@
if ("label" == propertyName) {
setScaling();
LabelToken[][] tokens = null;
+ int nbs = checkStringLength(bsSelected.length());
if (value instanceof Lst) {
Lst<SV> list = (Lst<SV>) value;
int n = list.size();
tokens = new LabelToken[][] { null };
- for (int pt = 0, i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i =
bsSelected
+ for (int pt = 0, i = bsSelected.nextSetBit(0); i >= 0 && i < nbs; i =
bsSelected
.nextSetBit(i + 1)) {
if (pt >= n) {
setLabel(nullToken, "", i, true);
- return;
+ continue;
}
tokens[0] = null;
setLabel(tokens, SV.sValue(list.get(pt++)), i, true);
@@ -160,19 +164,16 @@
return;
}
-// see label:
-// if ("labels" == propertyName) {
-// setScaling();
-// Lst<String> labels = (Lst<String>) value;
-// for (int i = bsSelected.nextSetBit(0), pt = 0; i >= 0 && i < ac; i =
bsSelected
-// .nextSetBit(i + 1)) {
-// String strLabel = labels.get(pt++);
-// LabelToken[][] tokens = (strLabel == null || strLabel.length() == 0
? nullToken
-// : new LabelToken[][] { null });
-// setLabel(tokens, strLabel, i, true);
-// }
-// return;
-// }
+ if (propertyName.startsWith("label:")) {
+ // from @1.label = "xxx"
+ setScaling();
+ // in principle, we could make this more efficient,
+ // it would be at the cost of general atom property setting
+ checkStringLength(ac);
+ setLabel(new LabelToken[][] { null }, propertyName.substring(6),
+ ((Integer) value).intValue(), false);
+ return;
+ }
if ("clearBoxes" == propertyName) {
labelBoxes = null;
@@ -187,12 +188,14 @@
if ("bgcolor" == propertyName) {
isActive = true;
if (bsBgColixSet == null)
- bsBgColixSet = new BS();
+ bsBgColixSet = BS.newN(ac);
short bgcolix = C.getColixO(value);
- if (!setDefaults)
- for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
+ if (!setDefaults) {
+ int n = checkBgColixLength(bgcolix, bsSelected.length());
+ for (int i = bsSelected.nextSetBit(0); i >= 0 && i < n; i = bsSelected
.nextSetBit(i + 1))
setBgcolix(i, bgcolix);
+ }
if (setDefaults || !defaultsOnlyForNone)
defaultBgcolix = bgcolix;
return;
@@ -201,7 +204,7 @@
// the rest require bsFontSet setting
if (bsFontSet == null)
- bsFontSet = new BS();
+ bsFontSet = BS.newN(ac);
if ("fontsize" == propertyName) {
int fontsize = ((Integer) value).intValue();
@@ -232,10 +235,11 @@
if ("offset" == propertyName) {
if (!(value instanceof Integer)) {
- if (!setDefaults)
+ if (!setDefaults) {
for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i =
bsSelected
.nextSetBit(i + 1))
setPymolOffset(i, (float[]) value);
+ }
return;
}
@@ -250,12 +254,11 @@
}
if ("align" == propertyName) {
+ // note that if the label is not offset, this centers the label with
offset 0 0
String type = (String) value;
- int hAlignment = JC.TEXT_ALIGN_LEFT;
- if (type.equalsIgnoreCase("right"))
- hAlignment = JC.TEXT_ALIGN_RIGHT;
- else if (type.equalsIgnoreCase("center"))
- hAlignment = JC.TEXT_ALIGN_CENTER;
+ int hAlignment = (type.equalsIgnoreCase("right") ? JC.TEXT_ALIGN_RIGHT
+ : type.equalsIgnoreCase("center") ? JC.TEXT_ALIGN_CENTER
+ : JC.TEXT_ALIGN_LEFT);
for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
.nextSetBit(i + 1))
setHorizAlignment(i, hAlignment);
@@ -309,17 +312,19 @@
LabelToken[] tokensUNK = null;
String strLabel;
LabelToken[] tokens;
+ int nstr = checkStringLength(bsSelected.length());
+ short bgcolix = defaultBgcolix;
+ int nbg = checkBgColixLength(bgcolix, bsSelected.length());
+ short thisMad = (short) (mode >= 0 ? 1 : -1);
for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
.nextSetBit(i + 1)) {
Atom atom = atoms[i];
- if (formats == null || i >= formats.length)
- formats = AU.ensureLengthS(formats, i + 1);
- if (strings != null && strings.length > i && strings[i] != null) {
- mads[i] = (short) (mode == 0 && mads[i] < 0 || mode == 1 ? 1 : -1);
+ if (i < nstr && strings[i] != null) {
+ // an old string -- toggle
+ mads[i] = (short) (mode == 1 || mode == 0 && mads[i] < 0 ? 1 : -1);
} else {
- if (bsSizeSet == null)
- bsSizeSet = new BS();
- strings = AU.ensureLengthS(strings, i + 1);
+ // a new string -- turn on
+ mads[i] = thisMad;
if (atom.getGroup3(false).equals("UNK")) {
if (strLabelUNK == null) {
strLabelUNK = vwr.getStandardLabelFormat(1);
@@ -339,37 +344,20 @@
null, ptTemp);
formats[i] = strLabel;
bsSizeSet.set(i);
- if ((bsBgColixSet == null || !bsBgColixSet.get(i))
- && defaultBgcolix != 0)
+ if (i < nbg && !bsBgColixSet.get(i))
setBgcolix(i, defaultBgcolix);
- mads[i] = (short) (mode >= 0 ? 1 : -1);
}
setShapeVisibility(atom, strings != null && i < strings.length
&& strings[i] != null && mads[i] >= 0);
- // } else if (strings != null && atomIndex < strings.length) {
- // strings[atomIndex] = null;
}
return;
}
- if (propertyName.startsWith("label:")) {
- // from @1.label = "xxx"
- setScaling();
- setLabel(new LabelToken[1][], propertyName.substring(6),
- ((Integer) value).intValue(), false);
+ if ("pymolLabels" == propertyName) {
+ setPymolLabels((Map<Integer, Text>) value, bsSelected);
return;
}
- if ("textLabels" == propertyName) {
- // from PyMOL reader
- setScaling();
- Map<Integer, Text> labels = (Map<Integer, Text>) value;
- for (int i = bsSelected.nextSetBit(0); i >= 0 && i < ac; i = bsSelected
- .nextSetBit(i + 1))
- setTextLabel(i, labels.get(Integer.valueOf(i)), null);
- return;
- }
-
if (propertyName == "deleteModelAtoms") {
labelBoxes = null;
int firstAtomDeleted = ((int[]) ((Object[]) value)[2])[1];
@@ -392,10 +380,47 @@
}
+ private int checkStringLength(int n) {
+ n = Math.min(ac, n);
+ if (strings == null || n > strings.length) {
+ formats = AU.ensureLengthS(formats, n);
+ strings = AU.ensureLengthS(strings, n);
+ if (bsSizeSet == null)
+ bsSizeSet = BS.newN(n);
+ }
+ return n;
+ }
+
+ private int checkBgColixLength(short colix, int n) {
+ n = Math.min(ac, n);
+ if (colix == C.INHERIT_ALL)
+ return (bgcolixes == null ? 0 : bgcolixes.length);
+ if (bgcolixes == null || n > bgcolixes.length)
+ bgcolixes = AU.ensureLengthShort(bgcolixes, n);
+ return n;
+ }
+
+ private void setPymolLabels(Map<Integer, Text> labels, BS bsSelected) {
+ // from PyMOL reader
+ setScaling();
+ int n = checkStringLength(ac);
+ for (int i = bsSelected.nextSetBit(0); i >= 0 && i < n; i = bsSelected
+ .nextSetBit(i + 1))
+ setPymolLabel(i, labels.get(Integer.valueOf(i)), null);
+ }
+
+ /**
+ * Sets offset using PyMOL standard array;
+ * only operates in cases where label is already defined
+ *
+ * @param i
+ * @param value
+ */
private void setPymolOffset(int i, float[] value) {
+ // from PyMOL reader or from set labeloffset [...]
Text text = getLabel(i);
if (text == null) {
- if (strings == null || strings.length <= i || strings[i] == null)
+ if (strings == null || i >= strings.length || strings[i] == null)
return;
byte fid = (bsFontSet != null && bsFontSet.get(i) ? fids[i] : -1);
if (fid < 0)
@@ -403,9 +428,7 @@
text = Text.newLabel(vwr, Font.getFont3D(fid), strings[i],
getColix2(i, atoms[i], false), getColix2(i, atoms[i], true), 0,
scalePixelsPerMicron);
- setTextLabel(i, text, formats[i]);
- if (text == null)
- return;
+ setPymolLabel(i, text, formats[i]);
}
text.pymolOffset = value;
}
@@ -418,13 +441,13 @@
private void setScaling() {
isActive = true;
if (bsSizeSet == null)
- bsSizeSet = new BS();
+ bsSizeSet = BS.newN(ac);
isScaled = vwr.getBoolean(T.fontscaling);
scalePixelsPerMicron = (isScaled ? vwr
.getScalePixelsPerAngstrom(false) * 10000f : 0);
}
- private void setTextLabel(int i, Text t, String format) {
+ private void setPymolLabel(int i, Text t, String format) {
if (t == null)
return;
String label = t.getText();
@@ -438,6 +461,7 @@
}
private void setLabel(LabelToken[][] temp, String strLabel, int i, boolean
doAll) {
+ // checkStringLength must be first
Atom atom = atoms[i];
LabelToken[] tokens = temp[0];
if (tokens == null)
@@ -476,10 +500,6 @@
private boolean addString(Atom atom, int i, String label, String strLabel) {
setShapeVisibility(atom, label != null);
- if (strings == null || i >= strings.length)
- strings = AU.ensureLengthS(strings, i + 1);
- if (formats == null || i >= formats.length)
- formats = AU.ensureLengthS(formats, i + 1);
boolean notNull = (strLabel != null);
boolean isNew = (strings[i] == null);
strings[i] = label;
@@ -533,11 +553,6 @@
}
private void setBgcolix(int i, short bgcolix) {
- if (bgcolixes == null || i >= bgcolixes.length) {
- if (bgcolix == 0)
- return;
- bgcolixes = AU.ensureLengthShort(bgcolixes, i + 1);
- }
bgcolixes[i] = bgcolix;
bsBgColixSet.setBitTo(i, bgcolix != 0);
Text text = getLabel(i);
@@ -548,12 +563,10 @@
private void setOffsets(int i, int offset) {
if (offsets == null || i >= offsets.length) {
- if (offset == 0)
+ if (offset == JC.LABEL_DEFAULT_OFFSET)
return;
- offsets = AU.ensureLengthI(offsets, i + 1);
+ offsets = AU.ensureLengthI(offsets, ac);
}
- if (offset == 0)
- offset = JC.LABEL_DEFAULT_OFFSET;
offsets[i] = (offsets[i] & JC.LABEL_FLAGS) | offset;
Text text = getLabel(i);
@@ -563,10 +576,15 @@
private void setHorizAlignment(int i, int hAlign) {
if (offsets == null || i >= offsets.length) {
- if (hAlign == JC.TEXT_ALIGN_LEFT)
+ switch (hAlign) {
+ case JC.TEXT_ALIGN_NONE:
+ case JC.TEXT_ALIGN_LEFT:
return;
- offsets = AU.ensureLengthI(offsets, i + 1);
+ }
+ offsets = AU.ensureLengthI(offsets, ac);
}
+ if (hAlign == JC.TEXT_ALIGN_NONE)
+ hAlign = JC.TEXT_ALIGN_LEFT;
offsets[i] = JC.setHorizAlignment(offsets[i], hAlign);
Text text = getLabel(i);
if (text != null)
@@ -577,7 +595,7 @@
if (offsets == null || i >= offsets.length) {
if (pointer == JC.LABEL_POINTER_NONE)
return;
- offsets = AU.ensureLengthI(offsets, i + 1);
+ offsets = AU.ensureLengthI(offsets, ac);
}
offsets[i] = JC.setPointer(offsets[i], pointer);
Text text = getLabel(i);
@@ -589,7 +607,7 @@
if (offsets == null || i >= offsets.length) {
if (!TF)
return;
- offsets = AU.ensureLengthI(offsets, i + 1);
+ offsets = AU.ensureLengthI(offsets, ac);
}
offsets[i] = JC.setZPosition(offsets[i], TF ? flag : 0);
}
@@ -598,7 +616,7 @@
if (fids == null || i >= fids.length) {
if (fid == zeroFontId)
return;
- fids = AU.ensureLengthByte(fids, i + 1);
+ fids = AU.ensureLengthByte(fids, ac);
}
fids[i] = fid;
bsFontSet.set(i);
Modified: branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties
===================================================================
--- branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-15
23:16:31 UTC (rev 20891)
+++ branches/v14_4/Jmol/src/org/jmol/viewer/Jmol.properties 2015-12-17
18:58:19 UTC (rev 20892)
@@ -7,8 +7,12 @@
# see also http://chemapps.stolaf.edu/jmol/zip for daily updates
-Jmol.___JmolVersion="14.4.1_2015.12.15"
+Jmol.___JmolVersion="14.5.1_2015.12.16"
+bug fix: array handling for labels very inefficient
+
+JmolVersion="14.4.1_2015.12.15"
+
bug fix: Bad build for Jmol Java applet
JmolVersion="14.4.1_2015.12.14"
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