Reverse abbreviation labels with numbered brackets correctly, B(OH)2 …

…becomes (HO)2B not 2(HO)B. Add recent reduce method needed for tests to pass.
cdk · Sep 16, 2016 · a3ddccb · a3ddccb
1 parent a9062d7
commit a3ddccb
Show file tree

Hide file tree

Showing 2 changed files with 36 additions and 3 deletions.
diff --git a/...sic/src/main/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabel.java b/...sic/src/main/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabel.java
@@ -25,8 +25,10 @@
 
 import org.openscience.cdk.config.Elements;
 
+import java.util.ArrayDeque;
 import java.util.ArrayList;
 import java.util.Collections;
+import java.util.Deque;
 import java.util.List;
 
 /**
@@ -247,6 +249,13 @@ private static boolean failParse(String label, List<String> tokens) {
         return false;
     }
 
+    private static boolean isNumber(String str) {
+        for (int i = 0; i < str.length(); i++)
+            if (!isDigit(str.charAt(i)))
+                return false;
+        return true;
+    }
+
     /**
      * Reverse a list of tokens for display, flipping
      * brackets as needed.
@@ -255,11 +264,24 @@ private static boolean failParse(String label, List<String> tokens) {
      */
     static void reverse(List<String> tokens) {
         Collections.reverse(tokens);
-        // now flip brackets
+        // now flip brackets and move numbers
+        Deque<String> numbers = new ArrayDeque<>();
         for (int i = 0; i < tokens.size(); i++) {
             String token = tokens.get(i);
-            if (token.equals("(")) tokens.set(i, ")");
-            else if (token.equals(")")) tokens.set(i, "(");
+            if (token.equals("(")) {
+                tokens.set(i, ")");
+                tokens.add(i+1, numbers.pop());
+                i++;
+            }
+            else if (token.equals(")")) {
+                tokens.set(i, "(");
+                if (i>0 && isNumber(tokens.get(i - 1))) {
+                    numbers.push(tokens.remove(i - 1));
+                    i--;
+                } else {
+                    numbers.push("");
+                }
+            }
         }
     }
 

diff --git a/...src/test/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabelTest.java b/...src/test/java/org/openscience/cdk/renderer/generators/standard/AbbreviationLabelTest.java
@@ -101,6 +101,7 @@ public void formatFeacac3() {
         List<String> tokens = new ArrayList<>();
         assertTrue(AbbreviationLabel.parse("Fe(acac)3", tokens));
         List<AbbreviationLabel.FormattedText> formatted = AbbreviationLabel.format(tokens);
+        AbbreviationLabel.reduce(formatted, 0, formatted.size());
         assertThat(formatted.get(0).text, is("Fe(acac)"));
         assertThat(formatted.get(0).style, is(0));
         assertThat(formatted.get(1).text, is("3"));
@@ -132,6 +133,14 @@ public void reversingBrackets() {
         assertThat(Joiner.on("").join(tokens), is("H2C(OH2CH2C)N"));
     }
 
+    @Test
+    public void reversingBracketsWithNumbers() {
+        List<String> tokens = new ArrayList<>();
+        assertTrue(AbbreviationLabel.parse("B(OH)2", tokens));
+        AbbreviationLabel.reverse(tokens);
+        assertThat(Joiner.on("").join(tokens), is("(HO)2B"));
+    }
+
     @Test
     public void nonAbbreviationLabel() {
         List<String> tokens = new ArrayList<>();
@@ -143,6 +152,7 @@ public void nonAbbreviationLabel() {
     public void formatOPO3() {
         List<String> tokens = Arrays.asList("O", "P", "O3", "-2");
         List<AbbreviationLabel.FormattedText> texts = AbbreviationLabel.format(tokens);
+        AbbreviationLabel.reduce(texts, 0, texts.size());
         assertThat(texts.size(), is(3));
         assertThat(texts.get(0).text, is("OPO"));
         assertThat(texts.get(0).style, is(AbbreviationLabel.STYLE_NORMAL));
@@ -167,6 +177,7 @@ public void formatTBu() {
     public void formatOPO3H2() {
         List<String> tokens = Arrays.asList("O", "P", "O3", "H2");
         List<AbbreviationLabel.FormattedText> texts = AbbreviationLabel.format(tokens);
+        AbbreviationLabel.reduce(texts, 0, texts.size());
         assertThat(texts.size(), is(4));
         assertThat(texts.get(0).text, is("OPO"));
         assertThat(texts.get(0).style, is(0));