From af313c7a589c4b5e32246c5a21346ceede6d0f32 Mon Sep 17 00:00:00 2001
From: Dominik Demuth <dominik.demuth@physik.tu-darmstadt.de>
Date: Mon, 23 Jan 2023 18:45:42 +0100
Subject: [PATCH] GraceEditor now clears previously read graphs when calling;
 fixes T257

---
 src/gui_qt/io/gracereader.py  |  1 -
 src/nmreval/io/graceeditor.py | 15 ++++++++++-----
 2 files changed, 10 insertions(+), 6 deletions(-)

diff --git a/src/gui_qt/io/gracereader.py b/src/gui_qt/io/gracereader.py
index 6de6008..f563239 100644
--- a/src/gui_qt/io/gracereader.py
+++ b/src/gui_qt/io/gracereader.py
@@ -45,7 +45,6 @@ class QGraceReader(QtWidgets.QDialog, Ui_Dialog):
 
     def read(self, fname):
         self._reader.parse(fname)
-        print('halio', len(self._reader.graphs))
 
         for graphs in self._reader.graphs:
             item = QtWidgets.QTreeWidgetItem([f'Graph {graphs.idx} (Title "{graphs.get_property("title")}")'])
diff --git a/src/nmreval/io/graceeditor.py b/src/nmreval/io/graceeditor.py
index 59c25e9..61c27db 100644
--- a/src/nmreval/io/graceeditor.py
+++ b/src/nmreval/io/graceeditor.py
@@ -10,6 +10,7 @@ import numpy as np
 from numpy import log10
 
 from ..configs import config_paths
+from ..lib.logger import logger
 
 
 class GraceEditor:
@@ -65,6 +66,7 @@ class GraceEditor:
         self.regions = []
         self.graphs = []
         self.sets = []
+        self.graphs = []
 
     def new_graph(self):
         if self.file is None:
@@ -129,7 +131,7 @@ class GraceEditor:
                         self.drawing_objects.append(GraceDrawing())
                         self.drawing_objects[-1].append(line)
                     else:
-                        print('What happened with this line?', line.rstrip())
+                        logger.warn('What happened with this line?', line.rstrip())
 
                 elif current_pos == 'drawing':
                     if self._RE_REGION_START.match(line):
@@ -194,8 +196,11 @@ class GraceEditor:
     def _make_graph(self, line: str):
         m = self._RE_GRAPH_START.match(line)
         g_idx = int(m.group(1))
-        while g_idx != len(self.graphs):
-            self.graphs.append(GraceGraph(len(self.graphs)))
+        if g_idx < len(self.graphs):
+            # this assumes that graphs are ordered in agr file even if missing, e.g. we read gß, g1, g3, ...
+            while g_idx != len(self.graphs):
+                self.graphs.append(GraceGraph(len(self.graphs)))
+
         self.graphs.append(GraceGraph(g_idx))
 
         return 'graph'
@@ -229,7 +234,7 @@ class GraceEditor:
                 pos = 'in_colors'
                 cnt += 1
                 if (int(m['red']), int(m['green']), int(m['blue'])) == rgb:
-                    print(f'color already defined as {m["disp"]}')
+                    logger.info(f'color already defined as {m["disp"]}')
                     return m['id']
                 elif m['id'] == idx:
                     self.header[i] = f'@map color {idx} to {rgb}, "{name}"\n'
@@ -238,7 +243,7 @@ class GraceEditor:
                 # landing here for first mismatch after all colors
                 if idx is None:
                     if cnt >= 64:
-                        warnings.warn('Maximum numbers of color reached, color is not used by xmgrace')
+                        logger.warn('Maximum numbers of color reached, color is not used by xmgrace')
                     self.header.insert(i, f'@map color {cnt} to {rgb}, "{name}"\n')
                     return cnt
                 else: