[Cml-cvs] jumbo53/src/org/xmlcml/cml/element CMLBuilder.java, 1.2, 1.3 CMLFragmentList.java, 1.3, 1.4

[Peter Murray-R. <pe...@us...>]

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
***************
*** 1,5 ****
  package org.xmlcml.cml.element;
  
- import java.io.File;
  import java.io.IOException;
  import java.io.StringReader;
--- 1,4 ----