Bug #12264 Warnings & notices

git-svn-id: http://svn.php.net/repository/pear/packages/Science_Chemistry/trunk@314453 c90b9560-bf6c-de11-be94-00142212c4b1
jmcastagnetto · Aug 8, 2011 · a6eeb2f · a6eeb2f
1 parent 9735dc6
commit a6eeb2f
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Showing 4 changed files with 17 additions and 13 deletions.
diff --git a/Science/Chemistry/Atom_PDB.php b/Science/Chemistry/Atom_PDB.php
@@ -158,10 +158,12 @@ class Science_Chemistry_Atom_PDB extends Science_Chemistry_Atom {
     var $parent_residue;
 
 
-    function Science_Chemistry_Atom_PDB($atomrec, $residue="") {
+    function Science_Chemistry_Atom_PDB(&$atomrec, &$residue="") {
         // reference to containing residue
-        if (!empty($residue))
+        if (!empty($residue)) {
-            $this->parent_residue =& $residue;
+            $this->parent_residue = $residue;
+        }
+
         // process PDB atom record
         // no error checking, assumes correct and standard record
         $this->VALID = true;

diff --git a/Science/Chemistry/Macromolecule_PDB.php b/Science/Chemistry/Macromolecule_PDB.php
@@ -45,8 +45,8 @@ class Science_Chemistry_Macromolecule_PDB extends Science_Chemistry_Macromolecul
      * @see     parseResidues()
      */
     function Science_Chemistry_Macromolecule_PDB($pdb, $records, $pdbfile="") {
-        $this->pdb =& $pdb;
+        $this->pdb = $pdb;
-        $this->pdbfile =& $pdbfile;
+        $this->pdbfile = $pdbfile;
         $this->parseResidues($records);
     }
 
@@ -71,8 +71,8 @@ function parseResidues($records) {
         }
 
          foreach ($res_atoms as $mol_id => $atoms_list) {
-            $this->molecules[] =& new Science_Chemistry_Residue_PDB(&$this->pdb, 
+            $this->molecules[] =& new Science_Chemistry_Residue_PDB($this->pdb, 
-                                            &$atoms_list, &$this);
+                                            $atoms_list, $this);
             $this->num_molecules++;
         }
         return true;

diff --git a/Science/Chemistry/PDBFile.php b/Science/Chemistry/PDBFile.php
@@ -124,7 +124,7 @@ function parseFile($arr, $usemeta) {
         $header_re = "/^HEADER[[:space:]]+(([^[:space:]]+ )+)[[:space:]]+";
         $header_re .= "([0-9]{2}-[A-Z]{3}-[0-9]{2,4})[[:space:]]+[A-Z0-9]{4}/";
 
-        if (preg_match($header_re, $arr[0], &$regs)) {
+        if (preg_match($header_re, $arr[0], $regs)) {
             $this->class = trim($regs[1]);
             // put date in a more standard format
             $tmp = explode("-", $regs[3]);
@@ -164,7 +164,7 @@ function parseFile($arr, $usemeta) {
             // the flag
             if ($rectype == "ENDMDL") {
                 $this->macromolecules[] = new Science_Chemistry_Macromolecule_PDB($this->pdb, 
-                                                $tmparr, &$this);
+                                                $tmparr, $this);
                 $this->num_macromolecules++;
                 $flag = "endmodel";
                 $tmparr = array();
@@ -173,8 +173,8 @@ function parseFile($arr, $usemeta) {
         // if we got to the end without hitting a MODEL ... ENDMDL pair
         // add the only macromolecule in this file to the array
         if ($flag == "nomodel") {
-            $this->macromolecules[] = new Science_Chemistry_Macromolecule_PDB(&$this->pdb, 
+            $this->macromolecules[] = new Science_Chemistry_Macromolecule_PDB($this->pdb, 
-                                            &$tmparr, &$this);
+                                            $tmparr, $this);
             $this->num_macromolecules++;
         }
 	}

diff --git a/Science/Chemistry/Residue_PDB.php b/Science/Chemistry/Residue_PDB.php
@@ -95,8 +95,10 @@ class Science_Chemistry_Residue_PDB extends Science_Chemistry_Molecule {
      * @access  public
      */
     function Science_Chemistry_Residue_PDB($pdb, $atomrec_arr, $macromol="") {
-        for ($i=0; $i < count($atomrec_arr); $i++)
+        for ($i=0; $i < count($atomrec_arr); $i++) {
-            $this->atoms[] = new Science_Chemistry_Atom_PDB(&$atomrec_arr[$i], &$this);
+            $this->atoms[] = new Science_Chemistry_Atom_PDB($atomrec_arr[$i], $this);
+        }
+
         if (!empty($this->atoms)) {
             $this->VALID = true;
             $this->macromol =& $macromol;