Update of /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element
In directory sc8-pr-cvs4.sourceforge.net:/tmp/cvs-serv31396/src/org/xmlcml/cml/element
Modified Files:
CMLBuilder.java CMLFragmentList.java
Log Message:
latest examples
Index: CMLFragmentList.java
===================================================================
RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/CMLFragmentList.java,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** CMLFragmentList.java 7 Dec 2006 11:24:42 -0000 1.3
--- CMLFragmentList.java 13 Dec 2006 22:39:35 -0000 1.4
***************
*** 2,5 ****
--- 2,8 ----
package org.xmlcml.cml.element;
+ import java.util.ArrayList;
+ import java.util.List;
+
import nu.xom.Element;
import nu.xom.Elements;
***************
*** 98,101 ****
--- 101,111 ----
/** clone content of element with CountExpression and append.
* clones the element content and appends to original element content
+ * significant children can only be join-fragment-join-fragment...join
+ * if FragmentLIst occurs only once (either explicitly or after application of
+ * countExpression its contents are interpreted as
+ * [J*1-F1-J12-F2-J23-F3] and any trailing join is ignored
+ * if count is greater that one
+ * syntax should be [JP1-F1-J12-F2-J21]n
+ *
* @param element to process
* @throws CMLRuntimeException null element or bad attribute
***************
*** 106,113 ****
int count = cea.calculateCountExpression();
int nChild = this.getChildCount();
for (int i = 1; i < count; i++) {
for (int j = 0; j < nChild; j++) {
Node newChild = this.getChild(j).copy();
! if (newChild instanceof CMLJoin) {
CMLJoin join = (CMLJoin) newChild;
String[] att = join.getMoleculeRefs2();
--- 116,149 ----
int count = cea.calculateCountExpression();
int nChild = this.getChildCount();
+ if (nChild %2 != 1) {
+ throw new CMLRuntimeException("Must have odd number of join-frag-join children");
+ }
+ List<CMLJoin> joinList = new ArrayList<CMLJoin>();
+ List<CMLFragment> fragList = new ArrayList<CMLFragment>();
+ // make lists of Join and Fragment children; check they alternate JFJF...J
+ int nsig = 0;
+ for (int j = 0; j < nChild; j++) {
+ Node newChild = this.getChild(j).copy();
+ if (newChild instanceof CMLJoin) {
+ if (nsig %2 != 0) {
+ throw new CMLRuntimeException("unexpected JOIN after: "+nsig+" significant children");
+ }
+ joinList.add((CMLJoin) newChild);
+ nsig++;
+ } else if (newChild instanceof CMLFragment) {
+ if (nsig %2 != 1) {
+ throw new CMLRuntimeException("unexpected FRAG after: "+nsig+" significant children");
+ }
+ fragList.add((CMLFragment) newChild);
+ nsig++;
+ }
+ }
for (int i = 1; i < count; i++) {
for (int j = 0; j < nChild; j++) {
Node newChild = this.getChild(j).copy();
! if (nsig %2 == 0) {
! if (!(newChild instanceof CMLJoin)) {
! throw new CMLRuntimeException("expected JOIN found: "+newChild);
! }
CMLJoin join = (CMLJoin) newChild;
String[] att = join.getMoleculeRefs2();
Index: CMLBuilder.java
===================================================================
RCS file: /cvsroot/cml/jumbo53/src/org/xmlcml/cml/element/CMLBuilder.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** CMLBuilder.java 7 Dec 2006 22:21:51 -0000 1.2
--- CMLBuilder.java 13 Dec 2006 22:39:35 -0000 1.3
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*** 1,5 ****
package org.xmlcml.cml.element;
- import java.io.File;
import java.io.IOException;
import java.io.StringReader;
--- 1,4 ----
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