Revision: 5139
Author: hansonr
Date: 2006-05-18 10:13:03 -0700 (Thu, 18 May 2006)
ViewCVS: http://svn.sourceforge.net/jmol/?rev=5139&view=rev
Log Message:
-----------
bob200603 introduces wildcards for insertion
select 186^*;spacefill on
select 186^?;spacefill on
#above two are the same -- just the insertions at 186
select *^?;spacefill on;color yellow
#all insertions
select *^A;spacefill on;color blue
#all insertions with "A"
Modified Paths:
--------------
branches/bob200603/Jmol/src/org/jmol/viewer/Compiler.java
branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java
branches/bob200603/Jmol/src/org/jmol/viewer/Group.java
branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Compiler.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Compiler.java 2006-05-18
05:17:40 UTC (rev 5138)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Compiler.java 2006-05-18
17:13:03 UTC (rev 5139)
@@ -173,12 +173,15 @@
continue;
}
if (lookingAtSeqcode()) {
- int seqNum =
+ int seqNum =(script.charAt(ichToken) == '*' ? 0 :
Integer.parseInt(script.substring(ichToken,
- ichToken + cchToken - 2));
+ ichToken + cchToken - 2)));
char insertionCode = script.charAt(ichToken + cchToken - 1);
+ if (insertionCode == '*')
+ insertionCode = '?';
int seqcode = Group.getSeqcode(seqNum, insertionCode);
ltoken.addElement(new Token(Token.seqcode, seqcode, "seqcode"));
+ System.out.println("compiler ins code "+insertionCode);
continue;
}
if (lookingAtInteger((tokCommand & Token.negnums) != 0)) {
@@ -591,12 +594,18 @@
boolean lookingAtSeqcode() {
int ichT = ichToken;
char ch = ' ';
- while (ichT < cchScript && isDigit(ch = script.charAt(ichT)))
+ if (ichT + 1 < cchScript && script.charAt(ichT) == '*'
+ && script.charAt(ichT + 1) == '^') {
+ ch = '^';
++ichT;
+ } else {
+ while (ichT < cchScript && isDigit(ch = script.charAt(ichT)))
+ ++ichT;
+ }
if (ichT == ichToken || ichT + 2 > cchScript || ch != '^')
return false;
ch = script.charAt(++ichT);
- if (! isAlphabetic(ch))
+ if (ch != '*' && ch != '?' && !isAlphabetic(ch))
return false;
++ichT;
cchToken = ichT - ichToken;
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java 2006-05-18
05:17:40 UTC (rev 5138)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Frame.java 2006-05-18
17:13:03 UTC (rev 5139)
@@ -1960,9 +1960,21 @@
BitSet getSpecSeqcode(int seqcode) {
BitSet bsResno = new BitSet();
- for (int i = atomCount; --i >= 0;) {
- if (seqcode == atoms[i].getSeqcode())
- bsResno.set(i);
+ int seqNum = (seqcode >> 8);
+ if (Group.getInsertionCode(seqcode) == '?') {
+ for (int i = atomCount; --i >= 0;) {
+ int atomSeqcode = atoms[i].getSeqcode();
+ if ((seqNum == 0 || seqNum == (atomSeqcode >> 8))
+ && (atomSeqcode & 0xFF) != 0)
+ bsResno.set(i);
+ }
+ } else {
+ for (int i = atomCount; --i >= 0;) {
+ int atomSeqcode = atoms[i].getSeqcode();
+ if (seqcode == atoms[i].getSeqcode() || seqNum == 0
+ && seqcode == (atomSeqcode & 0xFF))
+ bsResno.set(i);
+ }
}
return bsResno;
}
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/Group.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/Group.java 2006-05-18
05:17:40 UTC (rev 5138)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/Group.java 2006-05-18
17:13:03 UTC (rev 5139)
@@ -192,7 +192,8 @@
return sequenceNumber;
if (! ((insertionCode >= 'A' && insertionCode <= 'Z') ||
(insertionCode >= 'a' && insertionCode <= 'z') ||
- (insertionCode >= '0' && insertionCode <= '9'))) {
+ (insertionCode >= '0' && insertionCode <= '9')) &&
+ insertionCode != '?') {
if (insertionCode != ' ' && insertionCode != '\0')
System.out.println("unrecognized insertionCode:" + insertionCode);
insertionCode = '\0';
@@ -214,6 +215,12 @@
return (char)(seqcode & 0xFF);
}
+ static char getInsertionCode(int seqcode) {
+ if (seqcode == Integer.MIN_VALUE)
+ return '\0';
+ return (char)(seqcode & 0xFF);
+ }
+
final void selectAtoms(BitSet bs) {
for (int i = firstAtomIndex; i <= lastAtomIndex; ++i)
bs.set(i);
Modified: branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
===================================================================
--- branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
2006-05-18 05:17:40 UTC (rev 5138)
+++ branches/bob200603/Jmol/src/org/jmol/viewer/JmolConstants.java
2006-05-18 17:13:03 UTC (rev 5139)
@@ -42,7 +42,7 @@
// for now, just update this by hand
// perhaps use ant filter later ... but mth doesn't like it :-(
public final static String copyright = "(C) 2006 Jmol Development";
- public final static String version = "10.x.02(branch bob200603)";
+ public final static String version = "10.x.03(branch bob200603)";
public final static String cvsDate = "$Date$";
public final static String date = cvsDate.substring(7, 23);
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